sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | bedtools 2.31.1+dfsg-1 (arm64) Sat, 25 Nov 2023 17:30:59 +0000 | +==============================================================================+ Package: bedtools Version: 2.31.1+dfsg-1 Source Version: 2.31.1+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-81e2fc60-03aa-4524-a426-5655d01d6161' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-an1kbw/resolver-iGMOLG' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [198 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-11-25-1407.52-F-2023-11-25-0804.06.pdiff [25.7 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-11-25-1407.52-F-2023-11-25-0804.06.pdiff [54.3 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-11-25-1407.52-F-2023-11-25-0804.06.pdiff [25.7 kB] Get:6 http://localhost:3142/debian sid/main arm64 Packages [9510 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-11-25-1407.52-F-2023-11-25-0804.06.pdiff [54.3 kB] Fetched 9915 kB in 3s (3764 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bash binutils binutils-common binutils-x86-64-linux-gnu libbinutils libctf-nobfd0 libctf0 libffi8 libgprofng0 libsframe1 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7909 kB of archives. After this operation, 3072 B of additional disk space will be used. Get:1 http://localhost:3142/debian sid/main amd64 bash amd64 5.2.21-1 [1492 kB] Get:2 http://localhost:3142/debian sid/main amd64 libffi8 amd64 3.4.4-2 [23.5 kB] Get:3 http://localhost:3142/debian sid/main amd64 libgprofng0 amd64 2.41-7 [767 kB] Get:4 http://localhost:3142/debian sid/main amd64 libctf0 amd64 2.41-7 [87.0 kB] Get:5 http://localhost:3142/debian sid/main amd64 libctf-nobfd0 amd64 2.41-7 [151 kB] Get:6 http://localhost:3142/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.41-7 [2218 kB] Get:7 http://localhost:3142/debian sid/main amd64 libbinutils amd64 2.41-7 [512 kB] Get:8 http://localhost:3142/debian sid/main amd64 binutils amd64 2.41-7 [80.3 kB] Get:9 http://localhost:3142/debian sid/main amd64 binutils-common amd64 2.41-7 [2504 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsframe1 amd64 2.41-7 [75.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7909 kB in 0s (168 MB/s) (Reading database ... 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Processing triggers for debianutils (5.14) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bedtools.git Please use: git clone https://salsa.debian.org/med-team/bedtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 14.6 MB of source archives. Get:1 http://localhost:3142/debian sid/main bedtools 2.31.1+dfsg-1 (dsc) [2230 B] Get:2 http://localhost:3142/debian sid/main bedtools 2.31.1+dfsg-1 (tar) [14.5 MB] Get:3 http://localhost:3142/debian sid/main bedtools 2.31.1+dfsg-1 (diff) [14.5 kB] Fetched 14.6 MB in 0s (186 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedtools-an1kbw/bedtools-2.31.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-an1kbw' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [764 B] Get:5 copy:/<>/apt_archive ./ Packages [807 B] Fetched 2180 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-13-aarch64-linux-gnu gcc-13-aarch64-linux-gnu-base gcc-13-base:arm64 gcc-13-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbz2-1.0:arm64 libbz2-dev:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:arm64 libgcc-13-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1 libncursesw6 libnsl-dev:arm64 libnsl2:arm64 libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3:arm64 libstdc++-11-dev:arm64 libstdc++-13-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 krb5-doc:arm64 krb5-user:arm64 liblzma-doc:arm64 libstdc++-11-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:arm64 libidn2-0:arm64 libarchive-cpio-perl krb5-locales:arm64 libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-13-aarch64-linux-gnu gcc-13-aarch64-linux-gnu-base gcc-13-base:arm64 gcc-13-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbz2-1.0:arm64 libbz2-dev:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:arm64 libgcc-13-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1 libncursesw6 libnsl-dev:arm64 libnsl2:arm64 libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3:arm64 libstdc++-11-dev:arm64 libstdc++-13-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:arm64 sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 108 MB of archives. After this operation, 443 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6 [15.3 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.6-3 [815 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.6-3 [2030 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.4-5+b1 [26.5 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:8 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4+20231121-1 [135 kB] Get:9 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-2 [69.0 kB] Get:10 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-2 [166 kB] Get:11 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.44.0-1 [881 kB] Get:12 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.6-3 [1812 kB] Get:13 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.6-3 [586 kB] Get:14 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.4-5+b1 [9492 B] Get:15 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.4-5+b1 [26.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:17 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2 [314 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2 [105 kB] Get:19 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2 [42.8 kB] Get:20 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-13+b1 [161 kB] Get:21 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:22 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get:23 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.2-6 [89.1 kB] Get:24 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:25 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-1 [1402 kB] Get:26 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:27 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:28 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:29 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:30 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:31 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-13 [496 kB] Get:32 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.41-7 [3381 kB] Get:33 http://localhost:3142/debian sid/main amd64 gcc-13-aarch64-linux-gnu-base amd64 13.2.0-7cross1 [41.0 kB] Get:34 http://localhost:3142/debian sid/main amd64 cpp-13-aarch64-linux-gnu amd64 13.2.0-7cross1 [9773 kB] Get:35 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:13.2.0-1 [4120 B] Get:36 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:37 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-7cross1 [36.6 kB] Get:38 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.37-12cross1 [1006 kB] Get:39 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 13.2.0-7cross1 [40.8 kB] Get:40 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 13.2.0-7cross1 [112 kB] Get:41 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 13.2.0-7cross1 [23.3 kB] Get:42 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 13.2.0-7cross1 [9888 B] Get:43 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 13.2.0-7cross1 [2407 kB] Get:44 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 13.2.0-7cross1 [1068 kB] Get:45 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 13.2.0-7cross1 [2278 kB] Get:46 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 13.2.0-7cross1 [575 kB] Get:47 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 13.2.0-7cross1 [979 kB] Get:48 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 13.2.0-7cross1 [1119 kB] Get:49 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-arm64-cross all 13.2.0-7cross1 [2233 kB] Get:50 http://localhost:3142/debian sid/main amd64 gcc-13-aarch64-linux-gnu amd64 13.2.0-7cross1 [19.2 MB] Get:51 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:13.2.0-1 [1468 B] Get:52 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 6.5.8-1cross1 [1990 kB] Get:53 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.37-12cross1 [1427 kB] Get:54 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-arm64-cross all 13.2.0-7cross1 [2138 kB] Get:55 http://localhost:3142/debian sid/main amd64 g++-13-aarch64-linux-gnu amd64 13.2.0-7cross1 [10.7 MB] Get:56 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:13.2.0-1 [1172 B] Get:57 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:58 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:60 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [686 kB] Get:61 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:62 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:63 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:65 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:66 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:68 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:69 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:70 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:71 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:72 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.10 [3484 B] Get:73 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.8 [82.1 kB] Get:74 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:75 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:76 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:77 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:78 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:79 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:80 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.190-1 [176 kB] Get:81 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:82 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-13+b1 [1301 kB] Get:83 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:84 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:85 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.8 [956 kB] Get:86 http://localhost:3142/debian sid/main arm64 gcc-11-base arm64 11.4.0-5 [40.1 kB] Get:87 http://localhost:3142/debian sid/main arm64 gcc-13-base arm64 13.2.0-7 [40.8 kB] Get:88 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 13.2.0-7 [40.8 kB] Get:89 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.37-12 [2325 kB] Get:90 http://localhost:3142/debian sid/main arm64 libasan6 arm64 11.4.0-5 [1951 kB] Get:91 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 13.2.0-7 [10.2 kB] Get:92 http://localhost:3142/debian sid/main arm64 libbz2-1.0 arm64 1.0.8-5+b1 [47.5 kB] Get:93 http://localhost:3142/debian sid/main arm64 linux-libc-dev arm64 6.5.10-1 [1992 kB] Get:94 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.36-2 [90.3 kB] Get:95 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-2 [121 kB] Get:96 http://localhost:3142/debian sid/main arm64 libkrb5support0 arm64 1.20.1-5 [32.5 kB] Get:97 http://localhost:3142/debian sid/main arm64 libcom-err2 arm64 1.47.0-2+b1 [19.9 kB] Get:98 http://localhost:3142/debian sid/main arm64 libk5crypto3 arm64 1.20.1-5 [79.9 kB] Get:99 http://localhost:3142/debian sid/main arm64 libkeyutils1 arm64 1.6.3-2 [8844 B] Get:100 http://localhost:3142/debian sid/main arm64 libssl3 arm64 3.0.12-2 [1811 kB] Get:101 http://localhost:3142/debian sid/main arm64 libkrb5-3 arm64 1.20.1-5 [315 kB] Get:102 http://localhost:3142/debian sid/main arm64 libgssapi-krb5-2 arm64 1.20.1-5 [124 kB] Get:103 http://localhost:3142/debian sid/main arm64 libtirpc3 arm64 1.3.4+ds-1 [77.9 kB] Get:104 http://localhost:3142/debian sid/main arm64 libnsl2 arm64 1.3.0-3 [37.5 kB] Get:105 http://localhost:3142/debian sid/main arm64 libtirpc-dev arm64 1.3.4+ds-1 [192 kB] Get:106 http://localhost:3142/debian sid/main arm64 libnsl-dev arm64 1.3.0-3 [66.3 kB] Get:107 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.37-12 [1431 kB] Get:108 http://localhost:3142/debian sid/main arm64 libbz2-dev arm64 1.0.8-5+b1 [31.5 kB] Get:109 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 13.2.0-7 [114 kB] Get:110 http://localhost:3142/debian sid/main arm64 libitm1 arm64 13.2.0-7 [23.8 kB] Get:111 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 13.2.0-7 [1069 kB] Get:112 http://localhost:3142/debian sid/main arm64 libtsan0 arm64 11.4.0-5 [1957 kB] Get:113 http://localhost:3142/debian sid/main arm64 libstdc++6 arm64 13.2.0-7 [623 kB] Get:114 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 13.2.0-7 [980 kB] Get:115 http://localhost:3142/debian sid/main arm64 libhwasan0 arm64 13.2.0-7 [1121 kB] Get:116 http://localhost:3142/debian sid/main arm64 libgcc-11-dev arm64 11.4.0-5 [929 kB] Get:117 http://localhost:3142/debian sid/main arm64 liblzma5 arm64 5.4.5-0.1 [233 kB] Get:118 http://localhost:3142/debian sid/main arm64 liblzma-dev arm64 5.4.5-0.1 [288 kB] Get:119 http://localhost:3142/debian sid/main arm64 libstdc++-11-dev arm64 11.4.0-5 [1940 kB] Get:120 http://localhost:3142/debian sid/main arm64 zlib1g arm64 1:1.3.dfsg-3 [83.7 kB] Get:121 http://localhost:3142/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3 [915 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 108 MB in 1s (178 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14614 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.6-3_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.6-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.6-3_amd64.deb ... Unpacking python3.11-minimal (3.11.6-3) ... Setting up libpython3.11-minimal:amd64 (3.11.6-3) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.6-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 14944 files and directories currently installed.) 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Setting up libsqlite3-0:amd64 (3.44.0-1) ... Setting up libmagic1:amd64 (1:5.45-2) ... Setting up linux-libc-dev:arm64 (6.5.10-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-13+b1) ... Setting up m4 (1.4.19-4) ... Setting up binutils-aarch64-linux-gnu (2.41-7) ... Setting up file (1:5.45-2) ... Setting up libyaml-perl (1.30-2) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up gcc-13-base:arm64 (13.2.0-7) ... Setting up gcc-13-cross-base (13.2.0-7cross1) ... Setting up libc6-arm64-cross (2.37-12cross1) ... Setting up autopoint (0.21-13) ... Setting up libitm1-arm64-cross (13.2.0-7cross1) ... Setting up libncursesw6:amd64 (6.4+20231121-1) ... Setting up autoconf (2.71-3) ... Setting up linux-libc-dev-arm64-cross (6.5.8-1cross1) ... Setting up sensible-utils (0.0.20) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up gcc-13-aarch64-linux-gnu-base:amd64 (13.2.0-7cross1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libelf1:amd64 (0.190-1) ... Setting up readline-common (8.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3) ... Setting up liblocale-gettext-perl (1.07-6) ... Setting up libgcc-s1-arm64-cross (13.2.0-7cross1) ... Setting up libatomic1-arm64-cross (13.2.0-7cross1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblsan0-arm64-cross (13.2.0-7cross1) ... Setting up libgomp1-arm64-cross (13.2.0-7cross1) ... Setting up gettext (0.21-13+b1) ... Setting up cpp-13-aarch64-linux-gnu (13.2.0-7cross1) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:amd64 (8.2-2) ... Setting up libhwasan0-arm64-cross (13.2.0-7cross1) ... Setting up libc6-dev-arm64-cross (2.37-12cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (13.2.0-7cross1) ... Setting up dh-autoreconf (20) ... Setting up cpp-aarch64-linux-gnu (4:13.2.0-1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libasan8-arm64-cross (13.2.0-7cross1) ... Setting up libtsan2-arm64-cross (13.2.0-7cross1) ... Setting up libubsan1-arm64-cross (13.2.0-7cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.6-3) ... Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-13-dev-arm64-cross (13.2.0-7cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libpython3-stdlib:amd64 (3.11.4-5+b1) ... Setting up python3.11 (3.11.6-3) ... Setting up debhelper (13.11.8) ... Setting up python3 (3.11.4-5+b1) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-7cross1) ... Setting up libstdc++-13-dev-arm64-cross (13.2.0-7cross1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-7cross1) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-arm64 (12.10) ... Setting up libgcc-s1:arm64 (13.2.0-7) ... Setting up libc6:arm64 (2.37-12) ... Setting up libhwasan0:arm64 (13.2.0-7) ... Setting up libbz2-1.0:arm64 (1.0.8-5+b1) ... Setting up libstdc++6:arm64 (13.2.0-7) ... Setting up liblsan0:arm64 (13.2.0-7) ... Setting up libitm1:arm64 (13.2.0-7) ... Setting up libtsan0:arm64 (11.4.0-5) ... Setting up libkeyutils1:arm64 (1.6.3-2) ... Setting up liblzma5:arm64 (5.4.5-0.1) ... Setting up libssl3:arm64 (3.0.12-2) ... Setting up zlib1g:arm64 (1:1.3.dfsg-3) ... Setting up libcrypt1:arm64 (1:4.4.36-2) ... Setting up libcom-err2:arm64 (1.47.0-2+b1) ... Setting up libgomp1:arm64 (13.2.0-7) ... Setting up libasan6:arm64 (11.4.0-5) ... Setting up libkrb5support0:arm64 (1.20.1-5) ... Setting up libatomic1:arm64 (13.2.0-7) ... Setting up libk5crypto3:arm64 (1.20.1-5) ... Setting up liblzma-dev:arm64 (5.4.5-0.1) ... Setting up libubsan1:arm64 (13.2.0-7) ... Setting up libgcc-11-dev:arm64 (11.4.0-5) ... Setting up libcrypt-dev:arm64 (1:4.4.36-2) ... Setting up libkrb5-3:arm64 (1.20.1-5) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-5) ... Setting up libtirpc3:arm64 (1.3.4+ds-1) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1) ... Setting up libnsl2:arm64 (1.3.0-3) ... Setting up libnsl-dev:arm64 (1.3.0-3) ... Setting up libc6-dev:arm64 (2.37-12) ... Setting up libbz2-dev:arm64 (1.0.8-5+b1) ... Setting up libstdc++-11-dev:arm64 (11.4.0-5) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.37-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64) Toolchain package versions: binutils_2.41-7 dpkg-dev_1.22.1 g++-11_11.4.0-5 g++-13_13.2.0-7 gcc-11_11.4.0-5 gcc-13_13.2.0-7 libc6-dev_2.37-12 libstdc++-11-dev_11.4.0-5 libstdc++-13-dev_13.2.0-7 libstdc++-13-dev-arm64-cross_13.2.0-7cross1 libstdc++6_13.2.0-7 libstdc++6-arm64-cross_13.2.0-7cross1 linux-libc-dev_6.5.10-1 Package versions: adduser_3.137 apt_2.7.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.2 bash_5.2.21-1 binutils_2.41-7 binutils-aarch64-linux-gnu_2.41-7 binutils-common_2.41-7 binutils-x86-64-linux-gnu_2.41-7 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.10 bzip2_1.0.8-5+b1 coreutils_9.4-2+b1 cpp_4:13.2.0-1 cpp-11_11.4.0-5 cpp-13_13.2.0-7 cpp-13-aarch64-linux-gnu_13.2.0-7cross1 cpp-aarch64-linux-gnu_4:13.2.0-1 cross-config_2.6.20 crossbuild-essential-arm64_12.10 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debian-archive-keyring_2023.4 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.1 dpkg-cross_2.6.20 dpkg-dev_1.22.1 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1 g++-11_11.4.0-5 g++-13_13.2.0-7 g++-13-aarch64-linux-gnu_13.2.0-7cross1 g++-aarch64-linux-gnu_4:13.2.0-1 gcc_4:13.2.0-1 gcc-11_11.4.0-5 gcc-11-base_11.4.0-5 gcc-12-base_12.3.0-11 gcc-13_13.2.0-7 gcc-13-aarch64-linux-gnu_13.2.0-7cross1 gcc-13-aarch64-linux-gnu-base_13.2.0-7cross1 gcc-13-base_13.2.0-7 gcc-13-cross-base_13.2.0-7cross1 gcc-9-base_9.5.0-4 gcc-aarch64-linux-gnu_4:13.2.0-1 gettext_0.21-13+b1 gettext-base_0.21-13+b1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.7 libarchive-zip-perl_1.68-1 libasan6_11.4.0-5 libasan8_13.2.0-7 libasan8-arm64-cross_13.2.0-7cross1 libatomic1_13.2.0-7 libatomic1-arm64-cross_13.2.0-7cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-7 libblkid1_2.39.2-6 libbz2-1.0_1.0.8-5+b1 libbz2-dev_1.0.8-5+b1 libc-bin_2.37-12 libc-dev-bin_2.37-12 libc6_2.37-12 libc6-arm64-cross_2.37-12cross1 libc6-dev_2.37-12 libc6-dev-arm64-cross_2.37-12cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-4 libcc1-0_13.2.0-7 libcom-err2_1.47.0-2+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 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all Version: 2.31.1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://github.com/arq5x/bedtools2 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bedtools Vcs-Git: https://salsa.debian.org/med-team/bedtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev Package-List: bedtools deb science optional arch=any bedtools-test deb science optional arch=all Checksums-Sha1: 9ba1fbd50bf0ecac6c33c034e3a5251175a719d2 14546540 bedtools_2.31.1+dfsg.orig.tar.xz a185997bd886f6f8bd889168d86d4e2fb52eaf3a 14464 bedtools_2.31.1+dfsg-1.debian.tar.xz Checksums-Sha256: a92f0cdf52481c7dd0158a7971b89949386ef62021c6c2f7723dcad03f530819 14546540 bedtools_2.31.1+dfsg.orig.tar.xz 24141283f39fa4f1fb260effaa60bad982cab73272b8d35b7f9469aa60c60342 14464 bedtools_2.31.1+dfsg-1.debian.tar.xz Files: 8b409503aaf8b0de729d101cb92022c6 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Fri Nov 24 11:21:39 2023 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting bedtools in /<> dpkg-source: info: unpacking bedtools_2.31.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bedtools_2.31.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gzstream.h.patch dpkg-source: info: applying remove_barski_binding_site.png.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying hardening dpkg-source: info: applying htsutil dpkg-source: info: applying no_ulimit.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.nMEmF4xfVn/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-81e2fc60-03aa-4524-a426-5655d01d6161 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.31.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from bedtools-2.31.1+dfsg/debian/source/options: --single-debian-patch debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' * Cleaning up. make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars debian/files rm -fr -- debian/bedtools/ debian/tmp/ debian/bedtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- VERBOSE=1 make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc VERBOSE=1 make[2]: Entering directory '/<>' Building BEDTools: ========================================================= CXXFLAGS is [-g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard] DETECTED_VERSION = v2.31.1 CURRENT_VERSION = Updating version file. * compiling src/bedtools.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedtools.o -MMD -MP -MF obj/bedtools.Td -c -o obj/bedtools.o src/bedtools.cpp * compiling src/htsutil.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/htsutil.o -MMD -MP -MF obj/htsutil.Td -c -o obj/htsutil.o src/htsutil.cpp * compiling src/annotateBed/annotateMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateMain.o -MMD -MP -MF obj/annotateMain.Td -c -o obj/annotateMain.o src/annotateBed/annotateMain.cpp * compiling src/annotateBed/annotateBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateBed.o -MMD -MP -MF obj/annotateBed.Td -c -o obj/annotateBed.o src/annotateBed/annotateBed.cpp * compiling src/bamToBed/bamToBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToBed.o -MMD -MP -MF obj/bamToBed.Td -c -o obj/bamToBed.o src/bamToBed/bamToBed.cpp src/bamToBed/bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’: src/bamToBed/bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable] 88 | bool useAlignmentScore = false; | ^~~~~~~~~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToBed/bamToBed.cpp:12: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/bamToFastq/bamToFastqMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastqMain.o -MMD -MP -MF obj/bamToFastqMain.Td -c -o obj/bamToFastqMain.o src/bamToFastq/bamToFastqMain.cpp src/bamToFastq/bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’: src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable] 38 | bool haveFastq2 = false; | ^~~~~~~~~~ * compiling src/bamToFastq/bamToFastq.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastq.o -MMD -MP -MF obj/bamToFastq.Td -c -o obj/bamToFastq.o src/bamToFastq/bamToFastq.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToFastq/bamToFastq.h:15, from src/bamToFastq/bamToFastq.cpp:15: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/bedToBam/bedToBam.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToBam.o -MMD -MP -MF obj/bedToBam.Td -c -o obj/bedToBam.o src/bedToBam/bedToBam.cpp src/bedToBam/bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’: src/bedToBam/bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] 60 | bool haveMapQual = false; | ^~~~~~~~~~~ * compiling src/bedpeToBam/bedpeToBam.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedpeToBam.o -MMD -MP -MF obj/bedpeToBam.Td -c -o obj/bedpeToBam.o src/bedpeToBam/bedpeToBam.cpp src/bedpeToBam/bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’: src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] 61 | bool haveMapQual = false; | ^~~~~~~~~~~ * compiling src/bedToIgv/bedToIgv.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToIgv.o -MMD -MP -MF obj/bedToIgv.Td -c -o obj/bedToIgv.o src/bedToIgv/bedToIgv.cpp * compiling src/bed12ToBed6/bed12ToBed6.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bed12ToBed6.o -MMD -MP -MF obj/bed12ToBed6.Td -c -o obj/bed12ToBed6.o src/bed12ToBed6/bed12ToBed6.cpp * compiling src/closestFile/closestHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestHelp.o -MMD -MP -MF obj/closestHelp.Td -c -o obj/closestHelp.o src/closestFile/closestHelp.cpp * compiling src/closestFile/closestFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestFile.o -MMD -MP -MF obj/closestFile.Td -c -o obj/closestFile.o src/closestFile/closestFile.cpp * compiling src/clusterBed/clusterMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterMain.o -MMD -MP -MF obj/clusterMain.Td -c -o obj/clusterMain.o src/clusterBed/clusterMain.cpp src/clusterBed/clusterMain.cpp: In function ‘int cluster_main(int, char**)’: src/clusterBed/clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable] 38 | bool haveMaxDistance = false; | ^~~~~~~~~~~~~~~ * compiling src/clusterBed/clusterBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterBed.o -MMD -MP -MF obj/clusterBed.Td -c -o obj/clusterBed.o src/clusterBed/clusterBed.cpp * compiling src/complementFile/complementHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementHelp.o -MMD -MP -MF obj/complementHelp.Td -c -o obj/complementHelp.o src/complementFile/complementHelp.cpp * compiling src/complementFile/complementFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementFile.o -MMD -MP -MF obj/complementFile.Td -c -o obj/complementFile.o src/complementFile/complementFile.cpp * compiling src/coverageFile/coverageHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageHelp.o -MMD -MP -MF obj/coverageHelp.Td -c -o obj/coverageHelp.o src/coverageFile/coverageHelp.cpp * compiling src/coverageFile/coverageFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageFile.o -MMD -MP -MF obj/coverageFile.Td -c -o obj/coverageFile.o src/coverageFile/coverageFile.cpp src/coverageFile/coverageFile.cpp: In member function ‘virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)’: src/coverageFile/coverageFile.cpp:100:25: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | asprintf(&depthPctString, "%0.7f", depthPct); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)’: src/coverageFile/coverageFile.cpp:181:17: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 181 | asprintf(&meanString, "%0.7f", mean); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)’: src/coverageFile/coverageFile.cpp:210:25: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 210 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)’: src/coverageFile/coverageFile.cpp:230:17: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/expand/expand.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/expand.o -MMD -MP -MF obj/expand.Td -c -o obj/expand.o src/expand/expand.cpp * compiling src/fastaFromBed/fastaFromBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBedMain.o -MMD -MP -MF obj/fastaFromBedMain.Td -c -o obj/fastaFromBedMain.o src/fastaFromBed/fastaFromBedMain.cpp * compiling src/fastaFromBed/fastaFromBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBed.o -MMD -MP -MF obj/fastaFromBed.Td -c -o obj/fastaFromBed.o src/fastaFromBed/fastaFromBed.cpp * compiling src/flankBed/flankBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBedMain.o -MMD -MP -MF obj/flankBedMain.Td -c -o obj/flankBedMain.o src/flankBed/flankBedMain.cpp * compiling src/flankBed/flankBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBed.o -MMD -MP -MF obj/flankBed.Td -c -o obj/flankBed.o src/flankBed/flankBed.cpp * compiling src/genomeCoverageBed/genomeCoverageMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageMain.o -MMD -MP -MF obj/genomeCoverageMain.Td -c -o obj/genomeCoverageMain.o src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/genomeCoverageBed/genomeCoverageBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageBed.o -MMD -MP -MF obj/genomeCoverageBed.Td -c -o obj/genomeCoverageBed.o src/genomeCoverageBed/genomeCoverageBed.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/GenomeFile/NewGenomeFile.h:20, from src/genomeCoverageBed/genomeCoverageBed.h:13, from src/genomeCoverageBed/genomeCoverageBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/13/ios:44, from /usr/aarch64-linux-gnu/include/c++/13/istream:40, from /usr/aarch64-linux-gnu/include/c++/13/sstream:40, from src/utils/lineFileUtilities/lineFileUtilities.h:8, from src/genomeCoverageBed/genomeCoverageBed.cpp:12: In member function ‘std::streamsize std::ios_base::precision(std::streamsize)’, inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:541:23: /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:744:20: warning: ‘prec’ may be used uninitialized [-Wmaybe-uninitialized] 744 | _M_precision = __prec; | ~~~~~~~~~~~~~^~~~~~~~ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:491:16: note: ‘prec’ was declared here 491 | streamsize prec; | ^~~~ In function ‘constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)’, inlined from ‘const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)’ at /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:100:22, inlined from ‘std::ios_base::fmtflags std::ios_base::setf(fmtflags)’ at /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:692:19, inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:542:18: /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:88:71: warning: ‘fflags’ may be used uninitialized [-Wmaybe-uninitialized] 88 | { return _Ios_Fmtflags(static_cast(__a) | static_cast(__b)); } | ^ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:492:29: note: ‘fflags’ was declared here 492 | std::ios_base::fmtflags fflags; | ^~~~~~ In member function ‘std::streamsize std::ios_base::precision(std::streamsize)’, inlined from ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:401:27: /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:744:20: warning: ‘prec’ may be used uninitialized [-Wmaybe-uninitialized] 744 | _M_precision = __prec; | ~~~~~~~~~~~~~^~~~~~~~ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:381:20: note: ‘prec’ was declared here 381 | streamsize prec; | ^~~~ In function ‘constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)’, inlined from ‘const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)’ at /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:100:22, inlined from ‘std::ios_base::fmtflags std::ios_base::setf(fmtflags)’ at /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:692:19, inlined from ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:402:22: /usr/aarch64-linux-gnu/include/c++/13/bits/ios_base.h:88:71: warning: ‘fflags’ may be used uninitialized [-Wmaybe-uninitialized] 88 | { return _Ios_Fmtflags(static_cast(__a) | static_cast(__b)); } | ^ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:382:33: note: ‘fflags’ was declared here 382 | std::ios_base::fmtflags fflags; | ^~~~~~ * compiling src/getOverlap/getOverlap.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/getOverlap.o -MMD -MP -MF obj/getOverlap.Td -c -o obj/getOverlap.o src/getOverlap/getOverlap.cpp src/getOverlap/getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’: src/getOverlap/getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable] 44 | bool haveColumns = false; | ^~~~~~~~~~~ * compiling src/groupBy/groupByHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupByHelp.o -MMD -MP -MF obj/groupByHelp.Td -c -o obj/groupByHelp.o src/groupBy/groupByHelp.cpp * compiling src/groupBy/groupBy.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupBy.o -MMD -MP -MF obj/groupBy.Td -c -o obj/groupBy.o src/groupBy/groupBy.cpp * compiling src/intersectFile/intersectHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectHelp.o -MMD -MP -MF obj/intersectHelp.Td -c -o obj/intersectHelp.o src/intersectFile/intersectHelp.cpp * compiling src/intersectFile/intersectFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectFile.o -MMD -MP -MF obj/intersectFile.Td -c -o obj/intersectFile.o src/intersectFile/intersectFile.cpp * compiling src/fisher/fisherHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisherHelp.o -MMD -MP -MF obj/fisherHelp.Td -c -o obj/fisherHelp.o src/fisher/fisherHelp.cpp * compiling src/fisher/fisher.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisher.o -MMD -MP -MF obj/fisher.Td -c -o obj/fisher.o src/fisher/fisher.cpp * compiling src/fisher/kfunc.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/kfunc.o -MMD -MP -MF obj/kfunc.Td -c -o obj/kfunc.o src/fisher/kfunc.cpp * compiling src/jaccard/jaccardHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccardHelp.o -MMD -MP -MF obj/jaccardHelp.Td -c -o obj/jaccardHelp.o src/jaccard/jaccardHelp.cpp * compiling src/jaccard/jaccard.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccard.o -MMD -MP -MF obj/jaccard.Td -c -o obj/jaccard.o src/jaccard/jaccard.cpp * compiling src/linksBed/linksMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/linksMain.o -MMD -MP -MF obj/linksMain.Td -c -o obj/linksMain.o src/linksBed/linksMain.cpp * compiling src/linksBed/linksBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/linksBed.o -MMD -MP -MF obj/linksBed.Td -c -o obj/linksBed.o src/linksBed/linksBed.cpp * compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/maskFastaFromBedMain.o -MMD -MP -MF obj/maskFastaFromBedMain.Td -c -o obj/maskFastaFromBedMain.o src/maskFastaFromBed/maskFastaFromBedMain.cpp * compiling src/maskFastaFromBed/maskFastaFromBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/maskFastaFromBed.o -MMD -MP -MF obj/maskFastaFromBed.Td -c -o obj/maskFastaFromBed.o src/maskFastaFromBed/maskFastaFromBed.cpp * compiling src/mapFile/mapHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapHelp.o -MMD -MP -MF obj/mapHelp.Td -c -o obj/mapHelp.o src/mapFile/mapHelp.cpp * compiling src/mapFile/mapFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapFile.o -MMD -MP -MF obj/mapFile.Td -c -o obj/mapFile.o src/mapFile/mapFile.cpp * compiling src/mergeFile/mergeHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeHelp.o -MMD -MP -MF obj/mergeHelp.Td -c -o obj/mergeHelp.o src/mergeFile/mergeHelp.cpp * compiling src/mergeFile/mergeFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeFile.o -MMD -MP -MF obj/mergeFile.Td -c -o obj/mergeFile.o src/mergeFile/mergeFile.cpp * compiling src/multiBamCov/multiBamCovMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCovMain.o -MMD -MP -MF obj/multiBamCovMain.Td -c -o obj/multiBamCovMain.o src/multiBamCov/multiBamCovMain.cpp src/multiBamCov/multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’: src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable] 38 | bool haveBed = false; | ^~~~~~~ src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable] 39 | bool haveBams = false; | ^~~~~~~~ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 47 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/multiBamCov/multiBamCov.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCov.o -MMD -MP -MF obj/multiBamCov.Td -c -o obj/multiBamCov.o src/multiBamCov/multiBamCov.cpp In file included from src/utils/BamTools/include/BamReader.hpp:4, from src/utils/BamTools/include/api/BamMultiReader.h:4, from src/multiBamCov/multiBamCov.h:16, from src/multiBamCov/multiBamCov.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/multiIntersectBed/multiIntersectBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBedMain.o -MMD -MP -MF obj/multiIntersectBedMain.Td -c -o obj/multiIntersectBedMain.o src/multiIntersectBed/multiIntersectBedMain.cpp src/multiIntersectBed/multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’: src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] 45 | bool haveFiles = false; | ^~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] 47 | bool haveGenome = false; | ^~~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] 48 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/multiIntersectBed/multiIntersectBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBed.o -MMD -MP -MF obj/multiIntersectBed.Td -c -o obj/multiIntersectBed.o src/multiIntersectBed/multiIntersectBed.cpp * compiling src/nucBed/nucBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBedMain.o -MMD -MP -MF obj/nucBedMain.Td -c -o obj/nucBedMain.o src/nucBed/nucBedMain.cpp * compiling src/nucBed/nucBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBed.o -MMD -MP -MF obj/nucBed.Td -c -o obj/nucBed.o src/nucBed/nucBed.cpp * compiling src/pairToBed/pairToBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBedMain.o -MMD -MP -MF obj/pairToBedMain.Td -c -o obj/pairToBedMain.o src/pairToBed/pairToBedMain.cpp src/pairToBed/pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’: src/pairToBed/pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 43 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/pairToBed/pairToBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBed.o -MMD -MP -MF obj/pairToBed.Td -c -o obj/pairToBed.o src/pairToBed/pairToBed.cpp src/pairToBed/pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const std::string&)’: src/pairToBed/pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] 257 | CHRPOS spanLength = 0; | ^~~~~~~~~~ src/pairToBed/pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const std::string&)’: src/pairToBed/pairToBed.cpp:310:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] 310 | CHRPOS spanLength = 0; | ^~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/pairToBed/pairToBed.h:15, from src/pairToBed/pairToBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/pairToPair/pairToPairMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPairMain.o -MMD -MP -MF obj/pairToPairMain.Td -c -o obj/pairToPairMain.o src/pairToPair/pairToPairMain.cpp src/pairToPair/pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’: src/pairToPair/pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 44 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/pairToPair/pairToPair.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPair.o -MMD -MP -MF obj/pairToPair.Td -c -o obj/pairToPair.o src/pairToPair/pairToPair.cpp src/pairToPair/pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’: src/pairToPair/pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable] 112 | bool found1 = false; | ^~~~~~ src/pairToPair/pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable] 113 | bool found2 = false; | ^~~~~~ * compiling src/randomBed/randomBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBedMain.o -MMD -MP -MF obj/randomBedMain.Td -c -o obj/randomBedMain.o src/randomBed/randomBedMain.cpp * compiling src/randomBed/randomBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBed.o -MMD -MP -MF obj/randomBed.Td -c -o obj/randomBed.o src/randomBed/randomBed.cpp * compiling src/regressTest/regressTestMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/regressTestMain.o -MMD -MP -MF obj/regressTestMain.Td -c -o obj/regressTestMain.o src/regressTest/regressTestMain.cpp * compiling src/regressTest/RegressTest.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RegressTest.o -MMD -MP -MF obj/RegressTest.Td -c -o obj/RegressTest.o src/regressTest/RegressTest.cpp src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: src/regressTest/RegressTest.cpp:431:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 431 | system(diffCmd.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: src/regressTest/RegressTest.cpp:573:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 573 | fgets(sLine, 4192, fp); | ~~~~~^~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: src/regressTest/RegressTest.cpp:622:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 622 | fgets(sLine, 4192, fp); | ~~~~~^~~~~~~~~~~~~~~~~ * compiling src/reldist/reldistMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldistMain.o -MMD -MP -MF obj/reldistMain.Td -c -o obj/reldistMain.o src/reldist/reldistMain.cpp * compiling src/reldist/reldist.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldist.o -MMD -MP -MF obj/reldist.Td -c -o obj/reldist.o src/reldist/reldist.cpp src/reldist/reldist.cpp: In member function ‘void RelativeDistance::CalculateRelativeDistance()’: src/reldist/reldist.cpp:129:25: warning: comparison of integer expressions of different signedness: ‘CHRPOS’ {aka ‘long int’} and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 129 | if (low_idx != chrom_mids->size() - 1) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/sampleFile/sampleHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleHelp.o -MMD -MP -MF obj/sampleHelp.Td -c -o obj/sampleHelp.o src/sampleFile/sampleHelp.cpp * compiling src/sampleFile/sampleFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleFile.o -MMD -MP -MF obj/sampleFile.Td -c -o obj/sampleFile.o src/sampleFile/sampleFile.cpp * compiling src/shiftBed/shiftBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBedMain.o -MMD -MP -MF obj/shiftBedMain.Td -c -o obj/shiftBedMain.o src/shiftBed/shiftBedMain.cpp * compiling src/shiftBed/shiftBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBed.o -MMD -MP -MF obj/shiftBed.Td -c -o obj/shiftBed.o src/shiftBed/shiftBed.cpp * compiling src/shuffleBed/shuffleBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBedMain.o -MMD -MP -MF obj/shuffleBedMain.Td -c -o obj/shuffleBedMain.o src/shuffleBed/shuffleBedMain.cpp * compiling src/shuffleBed/shuffleBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBed.o -MMD -MP -MF obj/shuffleBed.Td -c -o obj/shuffleBed.o src/shuffleBed/shuffleBed.cpp * compiling src/slopBed/slopBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBedMain.o -MMD -MP -MF obj/slopBedMain.Td -c -o obj/slopBedMain.o src/slopBed/slopBedMain.cpp * compiling src/slopBed/slopBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBed.o -MMD -MP -MF obj/slopBed.Td -c -o obj/slopBed.o src/slopBed/slopBed.cpp * compiling src/sortBed/sortMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortMain.o -MMD -MP -MF obj/sortMain.Td -c -o obj/sortMain.o src/sortBed/sortMain.cpp * compiling src/sortBed/sortBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortBed.o -MMD -MP -MF obj/sortBed.Td -c -o obj/sortBed.o src/sortBed/sortBed.cpp * compiling src/spacingFile/spacingHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingHelp.o -MMD -MP -MF obj/spacingHelp.Td -c -o obj/spacingHelp.o src/spacingFile/spacingHelp.cpp * compiling src/spacingFile/spacingFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingFile.o -MMD -MP -MF obj/spacingFile.Td -c -o obj/spacingFile.o src/spacingFile/spacingFile.cpp * compiling src/split/splitBedMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBedMain.o -MMD -MP -MF obj/splitBedMain.Td -c -o obj/splitBedMain.o src/split/splitBedMain.cpp * compiling src/split/splitBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBed.o -MMD -MP -MF obj/splitBed.Td -c -o obj/splitBed.o src/split/splitBed.cpp * compiling src/subtractFile/subtractHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractHelp.o -MMD -MP -MF obj/subtractHelp.Td -c -o obj/subtractHelp.o src/subtractFile/subtractHelp.cpp * compiling src/subtractFile/subtractFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractFile.o -MMD -MP -MF obj/subtractFile.Td -c -o obj/subtractFile.o src/subtractFile/subtractFile.cpp * compiling src/summaryFile/summaryHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryHelp.o -MMD -MP -MF obj/summaryHelp.Td -c -o obj/summaryHelp.o src/summaryFile/summaryHelp.cpp * compiling src/summaryFile/summaryFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryFile.o -MMD -MP -MF obj/summaryFile.Td -c -o obj/summaryFile.o src/summaryFile/summaryFile.cpp * compiling src/tagBam/tagBamMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBamMain.o -MMD -MP -MF obj/tagBamMain.Td -c -o obj/tagBamMain.o src/tagBam/tagBamMain.cpp * compiling src/tagBam/tagBam.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBam.o -MMD -MP -MF obj/tagBam.Td -c -o obj/tagBam.o src/tagBam/tagBam.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/unionBedGraphs/unionBedGraphsMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphsMain.o -MMD -MP -MF obj/unionBedGraphsMain.Td -c -o obj/unionBedGraphsMain.o src/unionBedGraphs/unionBedGraphsMain.cpp src/unionBedGraphs/unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’: src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] 46 | bool haveFiles = false; | ^~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] 48 | bool haveGenome = false; | ^~~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] 49 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/unionBedGraphs/unionBedGraphs.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphs.o -MMD -MP -MF obj/unionBedGraphs.Td -c -o obj/unionBedGraphs.o src/unionBedGraphs/unionBedGraphs.cpp * compiling src/windowBed/windowMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMain.o -MMD -MP -MF obj/windowMain.Td -c -o obj/windowMain.o src/windowBed/windowMain.cpp * compiling src/windowBed/windowBed.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowBed.o -MMD -MP -MF obj/windowBed.Td -c -o obj/windowBed.o src/windowBed/windowBed.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/windowBed/windowBed.h:15, from src/windowBed/windowBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/windowMaker/windowMakerMain.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMakerMain.o -MMD -MP -MF obj/windowMakerMain.Td -c -o obj/windowMakerMain.o src/windowMaker/windowMakerMain.cpp * compiling src/windowMaker/windowMaker.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMaker.o -MMD -MP -MF obj/windowMaker.Td -c -o obj/windowMaker.o src/windowMaker/windowMaker.cpp * compiling src/utils/FileRecordTools/FileRecordMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMgr.o -MMD -MP -MF obj/FileRecordMgr.Td -c -o obj/FileRecordMgr.o src/utils/FileRecordTools/FileRecordMgr.cpp * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMergeMgr.o -MMD -MP -MF obj/FileRecordMergeMgr.Td -c -o obj/FileRecordMergeMgr.o src/utils/FileRecordTools/FileRecordMergeMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileReader.o -MMD -MP -MF obj/FileReader.Td -c -o obj/FileReader.o src/utils/FileRecordTools/FileReaders/FileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/SingleLineDelimTextFileReader.o -MMD -MP -MF obj/SingleLineDelimTextFileReader.Td -c -o obj/SingleLineDelimTextFileReader.o src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamFileReader.o -MMD -MP -MF obj/BamFileReader.Td -c -o obj/BamFileReader.o src/utils/FileRecordTools/FileReaders/BamFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BufferedStreamMgr.o -MMD -MP -MF obj/BufferedStreamMgr.Td -c -o obj/BufferedStreamMgr.o src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function ‘bool BufferedStreamMgr::readFileChunk()’: src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 148 | if (_mainBufCurrLen < _useBufSize) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/InputStreamMgr.o -MMD -MP -MF obj/InputStreamMgr.Td -c -o obj/InputStreamMgr.o src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Record.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Record.o -MMD -MP -MF obj/Record.Td -c -o obj/Record.o src/utils/FileRecordTools/Records/Record.cpp * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/EmptyRecord.o -MMD -MP -MF obj/EmptyRecord.Td -c -o obj/EmptyRecord.o src/utils/FileRecordTools/Records/EmptyRecord.cpp * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed3Interval.o -MMD -MP -MF obj/Bed3Interval.Td -c -o obj/Bed3Interval.o src/utils/FileRecordTools/Records/Bed3Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed4Interval.o -MMD -MP -MF obj/Bed4Interval.Td -c -o obj/Bed4Interval.o src/utils/FileRecordTools/Records/Bed4Interval.cpp * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedGraphInterval.o -MMD -MP -MF obj/BedGraphInterval.Td -c -o obj/BedGraphInterval.o src/utils/FileRecordTools/Records/BedGraphInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed5Interval.o -MMD -MP -MF obj/Bed5Interval.Td -c -o obj/Bed5Interval.o src/utils/FileRecordTools/Records/Bed5Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed6Interval.o -MMD -MP -MF obj/Bed6Interval.Td -c -o obj/Bed6Interval.o src/utils/FileRecordTools/Records/Bed6Interval.cpp * compiling src/utils/FileRecordTools/Records/PlusFields.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PlusFields.o -MMD -MP -MF obj/PlusFields.Td -c -o obj/PlusFields.o src/utils/FileRecordTools/Records/PlusFields.cpp * compiling src/utils/FileRecordTools/Records/GffRecord.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffRecord.o -MMD -MP -MF obj/GffRecord.Td -c -o obj/GffRecord.o src/utils/FileRecordTools/Records/GffRecord.cpp * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffPlusRecord.o -MMD -MP -MF obj/GffPlusRecord.Td -c -o obj/GffPlusRecord.o src/utils/FileRecordTools/Records/GffPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NoPosPlusRecord.o -MMD -MP -MF obj/NoPosPlusRecord.Td -c -o obj/NoPosPlusRecord.o src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedPlusInterval.o -MMD -MP -MF obj/BedPlusInterval.Td -c -o obj/BedPlusInterval.o src/utils/FileRecordTools/Records/BedPlusInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed12Interval.o -MMD -MP -MF obj/Bed12Interval.Td -c -o obj/Bed12Interval.o src/utils/FileRecordTools/Records/Bed12Interval.cpp * compiling src/utils/FileRecordTools/Records/BamRecord.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamRecord.o -MMD -MP -MF obj/BamRecord.Td -c -o obj/BamRecord.o src/utils/FileRecordTools/Records/BamRecord.cpp * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VcfRecord.o -MMD -MP -MF obj/VcfRecord.Td -c -o obj/VcfRecord.o src/utils/FileRecordTools/Records/VcfRecord.cpp * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockMgr.o -MMD -MP -MF obj/BlockMgr.Td -c -o obj/BlockMgr.o src/utils/FileRecordTools/Records/BlockMgr.cpp src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function ‘int BlockMgr::getNonRedundantOverlap()’: src/utils/FileRecordTools/Records/BlockMgr.cpp:194:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 194 | for (int i = 1; i < _overlapStarts.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/StrandQueue.o -MMD -MP -MF obj/StrandQueue.Td -c -o obj/StrandQueue.o src/utils/FileRecordTools/Records/StrandQueue.cpp * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordMgr.o -MMD -MP -MF obj/RecordMgr.Td -c -o obj/RecordMgr.o src/utils/FileRecordTools/Records/RecordMgr.cpp * compiling src/utils/FileRecordTools/Records/RecordList.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordList.o -MMD -MP -MF obj/RecordList.Td -c -o obj/RecordList.o src/utils/FileRecordTools/Records/RecordList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyList.o -MMD -MP -MF obj/RecordKeyList.Td -c -o obj/RecordKeyList.o src/utils/FileRecordTools/Records/RecordKeyList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyVector.o -MMD -MP -MF obj/RecordKeyVector.Td -c -o obj/RecordKeyVector.o src/utils/FileRecordTools/Records/RecordKeyVector.cpp * compiling src/utils/bedFile/bedFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFile.o -MMD -MP -MF obj/bedFile.Td -c -o obj/bedFile.o src/utils/bedFile/bedFile.cpp * compiling src/utils/BinTree/BinTree.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BinTree.o -MMD -MP -MF obj/BinTree.Td -c -o obj/BinTree.o src/utils/BinTree/BinTree.cpp * compiling src/utils/version/version.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/version.o -MMD -MP -MF obj/version.Td -c -o obj/version.o src/utils/version/version.cpp * compiling src/utils/bedGraphFile/bedGraphFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedGraphFile.o -MMD -MP -MF obj/bedGraphFile.Td -c -o obj/bedGraphFile.o src/utils/bedGraphFile/bedGraphFile.cpp * compiling src/utils/chromsweep/chromsweep.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/chromsweep.o -MMD -MP -MF obj/chromsweep.Td -c -o obj/chromsweep.o src/utils/chromsweep/chromsweep.cpp * compiling src/utils/Contexts/ContextBase.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextBase.o -MMD -MP -MF obj/ContextBase.Td -c -o obj/ContextBase.o src/utils/Contexts/ContextBase.cpp * compiling src/utils/Contexts/ContextIntersect.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextIntersect.o -MMD -MP -MF obj/ContextIntersect.Td -c -o obj/ContextIntersect.o src/utils/Contexts/ContextIntersect.cpp * compiling src/utils/Contexts/ContextFisher.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextFisher.o -MMD -MP -MF obj/ContextFisher.Td -c -o obj/ContextFisher.o src/utils/Contexts/ContextFisher.cpp * compiling src/utils/Contexts/ContextMap.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMap.o -MMD -MP -MF obj/ContextMap.Td -c -o obj/ContextMap.o src/utils/Contexts/ContextMap.cpp * compiling src/utils/Contexts/ContextSample.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSample.o -MMD -MP -MF obj/ContextSample.Td -c -o obj/ContextSample.o src/utils/Contexts/ContextSample.cpp * compiling src/utils/Contexts/ContextSpacing.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSpacing.o -MMD -MP -MF obj/ContextSpacing.Td -c -o obj/ContextSpacing.o src/utils/Contexts/ContextSpacing.cpp * compiling src/utils/Contexts/ContextMerge.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMerge.o -MMD -MP -MF obj/ContextMerge.Td -c -o obj/ContextMerge.o src/utils/Contexts/ContextMerge.cpp * compiling src/utils/Contexts/ContextJaccard.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextJaccard.o -MMD -MP -MF obj/ContextJaccard.Td -c -o obj/ContextJaccard.o src/utils/Contexts/ContextJaccard.cpp * compiling src/utils/Contexts/ContextClosest.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextClosest.o -MMD -MP -MF obj/ContextClosest.Td -c -o obj/ContextClosest.o src/utils/Contexts/ContextClosest.cpp * compiling src/utils/Contexts/ContextSubtract.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSubtract.o -MMD -MP -MF obj/ContextSubtract.Td -c -o obj/ContextSubtract.o src/utils/Contexts/ContextSubtract.cpp * compiling src/utils/Contexts/ContextCoverage.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextCoverage.o -MMD -MP -MF obj/ContextCoverage.Td -c -o obj/ContextCoverage.o src/utils/Contexts/ContextCoverage.cpp * compiling src/utils/Contexts/ContextComplement.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextComplement.o -MMD -MP -MF obj/ContextComplement.Td -c -o obj/ContextComplement.o src/utils/Contexts/ContextComplement.cpp * compiling src/utils/Contexts/ContextGroupBy.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextGroupBy.o -MMD -MP -MF obj/ContextGroupBy.Td -c -o obj/ContextGroupBy.o src/utils/Contexts/ContextGroupBy.cpp * compiling src/utils/Contexts/ContextSummary.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSummary.o -MMD -MP -MF obj/ContextSummary.Td -c -o obj/ContextSummary.o src/utils/Contexts/ContextSummary.cpp * compiling src/utils/general/ParseTools.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ParseTools.o -MMD -MP -MF obj/ParseTools.Td -c -o obj/ParseTools.o src/utils/general/ParseTools.cpp * compiling src/utils/general/PushBackStreamBuf.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PushBackStreamBuf.o -MMD -MP -MF obj/PushBackStreamBuf.Td -c -o obj/PushBackStreamBuf.o src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CompressionTools.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CompressionTools.o -MMD -MP -MF obj/CompressionTools.Td -c -o obj/CompressionTools.o src/utils/general/CompressionTools.cpp * compiling src/utils/general/Tokenizer.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Tokenizer.o -MMD -MP -MF obj/Tokenizer.Td -c -o obj/Tokenizer.o src/utils/general/Tokenizer.cpp * compiling src/utils/general/CommonHelp.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CommonHelp.o -MMD -MP -MF obj/CommonHelp.Td -c -o obj/CommonHelp.o src/utils/general/CommonHelp.cpp * compiling src/utils/general/ErrorMsg.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ErrorMsg.o -MMD -MP -MF obj/ErrorMsg.Td -c -o obj/ErrorMsg.o src/utils/general/ErrorMsg.cpp * compiling src/utils/general/Random.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Random.o -MMD -MP -MF obj/Random.Td -c -o obj/Random.o src/utils/general/Random.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Isrc/utils/gzstream -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/gzstream.o src/utils/gzstream/gzstream.C * compiling src/utils/fileType/fileType.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fileType.o -MMD -MP -MF obj/fileType.Td -c -o obj/fileType.o src/utils/fileType/fileType.cpp * compiling src/utils/fileType/FileRecordTypeChecker.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordTypeChecker.o -MMD -MP -MF obj/FileRecordTypeChecker.Td -c -o obj/FileRecordTypeChecker.o src/utils/fileType/FileRecordTypeChecker.cpp src/utils/fileType/FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’: src/utils/fileType/FileRecordTypeChecker.cpp:366:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 366 | for (int j=0; j < len; j++) { | ~~^~~~~ * compiling src/utils/bedFilePE/bedFilePE.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFilePE.o -MMD -MP -MF obj/bedFilePE.Td -c -o obj/bedFilePE.o src/utils/bedFilePE/bedFilePE.cpp * compiling src/utils/KeyListOps/KeyListOps.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOps.o -MMD -MP -MF obj/KeyListOps.Td -c -o obj/KeyListOps.o src/utils/KeyListOps/KeyListOps.cpp * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOpsMethods.o -MMD -MP -MF obj/KeyListOpsMethods.Td -c -o obj/KeyListOpsMethods.o src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewChromsweep.o -MMD -MP -MF obj/NewChromsweep.Td -c -o obj/NewChromsweep.o src/utils/NewChromsweep/NewChromsweep.cpp * compiling src/utils/NewChromsweep/CloseSweep.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CloseSweep.o -MMD -MP -MF obj/CloseSweep.Td -c -o obj/CloseSweep.o src/utils/NewChromsweep/CloseSweep.cpp * compiling src/utils/sequenceUtilities/sequenceUtils.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sequenceUtils.o -MMD -MP -MF obj/sequenceUtils.Td -c -o obj/sequenceUtils.o src/utils/sequenceUtilities/sequenceUtils.cpp * compiling src/utils/tabFile/tabFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tabFile.o -MMD -MP -MF obj/tabFile.Td -c -o obj/tabFile.o src/utils/tabFile/tabFile.cpp * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamAncillary.o -MMD -MP -MF obj/BamAncillary.Td -c -o obj/BamAncillary.o src/utils/BamTools-Ancillary/BamAncillary.cpp * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockedIntervals.o -MMD -MP -MF obj/BlockedIntervals.Td -c -o obj/BlockedIntervals.o src/utils/BlockedIntervals/BlockedIntervals.cpp * compiling src/utils/Fasta/Fasta.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Fasta.o -MMD -MP -MF obj/Fasta.Td -c -o obj/Fasta.o src/utils/Fasta/Fasta.cpp * compiling src/utils/Fasta/split.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/split.o -MMD -MP -MF obj/split.Td -c -o obj/split.o src/utils/Fasta/split.cpp * compiling src/utils/VectorOps/VectorOps.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VectorOps.o -MMD -MP -MF obj/VectorOps.Td -c -o obj/VectorOps.o src/utils/VectorOps/VectorOps.cpp * compiling src/utils/GenomeFile/NewGenomeFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewGenomeFile.o -MMD -MP -MF obj/NewGenomeFile.Td -c -o obj/NewGenomeFile.o src/utils/GenomeFile/NewGenomeFile.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GenomeFile.o -MMD -MP -MF obj/GenomeFile.Td -c -o obj/GenomeFile.o src/utils/GenomeFile/GenomeFile.cpp src/utils/GenomeFile/GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 60 | long c2; | ^~ * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordOutputMgr.o -MMD -MP -MF obj/RecordOutputMgr.Td -c -o obj/RecordOutputMgr.o src/utils/RecordOutputMgr/RecordOutputMgr.cpp src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector*)’: src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 170 | if (context->getNumClosestHitsWanted() > keyList.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)’: src/utils/RecordOutputMgr/RecordOutputMgr.cpp:456:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 456 | for (size_t i = 0; i < _context->getNumInputFiles(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/ToolBase/ToolBase.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ToolBase.o -MMD -MP -MF obj/ToolBase.Td -c -o obj/ToolBase.o src/utils/ToolBase/ToolBase.cpp * compiling src/utils/driver/BedtoolsDriver.cpp aarch64-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedtoolsDriver.o -MMD -MP -MF obj/BedtoolsDriver.Td -c -o obj/BedtoolsDriver.o src/utils/driver/BedtoolsDriver.cpp cd src/utils/htslib && make config.h make[3]: Entering directory '/<>/src/utils/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h make[3]: Leaving directory '/<>/src/utils/htslib' cd src/utils/htslib && make lib-static make[3]: Entering directory '/<>/src/utils/htslib' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c hts.c: In function ‘hts_idx_init’: hts.c:1397:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1397 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a make[3]: Leaving directory '/<>/src/utils/htslib' - Building main bedtools binary. aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o bin/bedtools obj/bedtools.o obj/htsutil.o obj/annotateMain.o obj/annotateBed.o obj/bamToBed.o obj/bamToFastqMain.o obj/bamToFastq.o obj/bedToBam.o obj/bedpeToBam.o obj/bedToIgv.o obj/bed12ToBed6.o obj/closestHelp.o obj/closestFile.o obj/clusterMain.o obj/clusterBed.o obj/complementHelp.o obj/complementFile.o obj/coverageHelp.o obj/coverageFile.o obj/expand.o obj/fastaFromBedMain.o obj/fastaFromBed.o obj/flankBedMain.o obj/flankBed.o obj/genomeCoverageMain.o obj/genomeCoverageBed.o obj/getOverlap.o obj/groupByHelp.o obj/groupBy.o obj/intersectHelp.o obj/intersectFile.o obj/fisherHelp.o obj/fisher.o obj/kfunc.o obj/jaccardHelp.o obj/jaccard.o obj/linksMain.o obj/linksBed.o obj/maskFastaFromBedMain.o obj/maskFastaFromBed.o obj/mapHelp.o obj/mapFile.o obj/mergeHelp.o obj/mergeFile.o obj/multiBamCovMain.o obj/multiBamCov.o obj/multiIntersectBedMain.o obj/multiIntersectBed.o obj/nucBedMain.o obj/nucBed.o obj/pairToBedMain.o obj/pairToBed.o obj/pairToPairMain.o obj/pairToPair.o obj/randomBedMain.o obj/randomBed.o obj/regressTestMain.o obj/RegressTest.o obj/reldistMain.o obj/reldist.o obj/sampleHelp.o obj/sampleFile.o obj/shiftBedMain.o obj/shiftBed.o obj/shuffleBedMain.o obj/shuffleBed.o obj/slopBedMain.o obj/slopBed.o obj/sortMain.o obj/sortBed.o obj/spacingHelp.o obj/spacingFile.o obj/splitBedMain.o obj/splitBed.o obj/subtractHelp.o obj/subtractFile.o obj/summaryHelp.o obj/summaryFile.o obj/tagBamMain.o obj/tagBam.o obj/unionBedGraphsMain.o obj/unionBedGraphs.o obj/windowMain.o obj/windowBed.o obj/windowMakerMain.o obj/windowMaker.o obj/FileRecordMgr.o obj/FileRecordMergeMgr.o obj/FileReader.o obj/SingleLineDelimTextFileReader.o obj/BamFileReader.o obj/BufferedStreamMgr.o obj/InputStreamMgr.o obj/Record.o obj/EmptyRecord.o obj/Bed3Interval.o obj/Bed4Interval.o obj/BedGraphInterval.o obj/Bed5Interval.o obj/Bed6Interval.o obj/PlusFields.o obj/GffRecord.o obj/GffPlusRecord.o obj/NoPosPlusRecord.o obj/BedPlusInterval.o obj/Bed12Interval.o obj/BamRecord.o obj/VcfRecord.o obj/BlockMgr.o obj/StrandQueue.o obj/RecordMgr.o obj/RecordList.o obj/RecordKeyList.o obj/RecordKeyVector.o obj/bedFile.o obj/BinTree.o obj/version.o obj/bedGraphFile.o obj/chromsweep.o obj/ContextBase.o obj/ContextIntersect.o obj/ContextFisher.o obj/ContextMap.o obj/ContextSample.o obj/ContextSpacing.o obj/ContextMerge.o obj/ContextJaccard.o obj/ContextClosest.o obj/ContextSubtract.o obj/ContextCoverage.o obj/ContextComplement.o obj/ContextGroupBy.o obj/ContextSummary.o obj/ParseTools.o obj/PushBackStreamBuf.o obj/CompressionTools.o obj/Tokenizer.o obj/CommonHelp.o obj/ErrorMsg.o obj/Random.o obj/gzstream.o obj/fileType.o obj/FileRecordTypeChecker.o obj/bedFilePE.o obj/KeyListOps.o obj/KeyListOpsMethods.o obj/NewChromsweep.o obj/CloseSweep.o obj/sequenceUtils.o obj/tabFile.o obj/BamAncillary.o obj/BlockedIntervals.o obj/Fasta.o obj/split.o obj/VectorOps.o obj/NewGenomeFile.o obj/GenomeFile.o obj/RecordOutputMgr.o obj/ToolBase.o obj/BedtoolsDriver.o src/utils/htslib/libhts.a -lz -lm -lbz2 -llzma -lpthread done. - Creating executables for old CLI. done. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/bedtools.substvars rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/ rm -f debian/bedtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- VERBOSE=1 install -m0755 -d /<>/bedtools-2.31.1\+dfsg/debian/tmp make -j1 install DESTDIR=/<>/bedtools-2.31.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>' mkdir -p /<>/debian/tmp/usr/local/bin for file in bin/* ; do \ cp -f $file /<>/debian/tmp/usr/local/bin; \ done make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/bedtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -m0755 -d debian/bedtools/usr/bin cp --reflink=auto -a debian/tmp/usr/local/bin/annotateBed debian/tmp/usr/local/bin/bamToBed debian/tmp/usr/local/bin/bamToFastq debian/tmp/usr/local/bin/bed12ToBed6 debian/tmp/usr/local/bin/bedToBam debian/tmp/usr/local/bin/bedToIgv debian/tmp/usr/local/bin/bedpeToBam debian/tmp/usr/local/bin/bedtools debian/tmp/usr/local/bin/closestBed debian/tmp/usr/local/bin/clusterBed debian/tmp/usr/local/bin/complementBed debian/tmp/usr/local/bin/coverageBed debian/tmp/usr/local/bin/expandCols debian/tmp/usr/local/bin/fastaFromBed debian/tmp/usr/local/bin/flankBed debian/tmp/usr/local/bin/genomeCoverageBed debian/tmp/usr/local/bin/getOverlap debian/tmp/usr/local/bin/groupBy debian/tmp/usr/local/bin/intersectBed debian/tmp/usr/local/bin/linksBed debian/tmp/usr/local/bin/mapBed debian/tmp/usr/local/bin/maskFastaFromBed debian/tmp/usr/local/bin/mergeBed debian/tmp/usr/local/bin/multiBamCov debian/tmp/usr/local/bin/multiIntersectBed debian/tmp/usr/local/bin/nucBed debian/tmp/usr/local/bin/pairToBed debian/tmp/usr/local/bin/pairToPair debian/tmp/usr/local/bin/randomBed debian/tmp/usr/local/bin/shiftBed debian/tmp/usr/local/bin/shuffleBed debian/tmp/usr/local/bin/slopBed debian/tmp/usr/local/bin/sortBed debian/tmp/usr/local/bin/subtractBed debian/tmp/usr/local/bin/tagBam debian/tmp/usr/local/bin/unionBedGraphs debian/tmp/usr/local/bin/windowBed debian/tmp/usr/local/bin/windowMaker debian/bedtools/usr/bin/ install -m0755 -d debian/bedtools/usr/share/bash-completion/completions cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools/usr/share/bash-completion/completions/ install -m0755 -d debian/bedtools/usr/share/bedtools cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/ # make sure all *.sh files are featuring a '#!/bin/bash' as first line # since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh} # requiring bash this is taken for all scripts instead of checking first via /bin/sh -n for sh in `find /<>/debian -name "*.sh"` ; do \ if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \ sed -i '1 i #!/bin/bash' ${sh} ; \ fi ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a install -m0755 -d debian/bedtools/usr/share/doc/bedtools install -m0755 -d debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright dh_installchangelogs -a install -m0755 -d debian/bedtools/usr/share/doc/bedtools install -p -m0644 debian/.debhelper/generated/bedtools/dh_installchangelogs.dch.trimmed debian/bedtools/usr/share/doc/bedtools/changelog.Debian dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/bedtools chmod a-x usr/share/doc/bedtools/changelog.Debian gzip -9nf usr/share/doc/bedtools/changelog.Debian cd '/<>' rm -f debian/bedtools.debhelper.log debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>' dh_fixperms find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x chmod -x /<>/debian/bedtools/usr/share/bedtools/genomes/*.genome find /<>/debian -name "*.bed" -executable -exec chmod -x \{\} \; find /<>/debian -name "*.sam" -executable -exec chmod -x \{\} \; find /<>/debian -name "*.sh" -not -executable -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dwz -- debian/bedtools/usr/bin/bedtools dh_strip -a install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/ed aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/ed/72a9e8c987581c53f9e8dd5e39db5d003fbcee.debug chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/ed/72a9e8c987581c53f9e8dd5e39db5d003fbcee.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/ed/72a9e8c987581c53f9e8dd5e39db5d003fbcee.debug debian/bedtools/usr/bin/bedtools install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym install -m0755 -d debian/.debhelper/bedtools dh_makeshlibs -a rm -f debian/bedtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/bedtools/DEBIAN dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_installdeb -a install -m0755 -d debian/bedtools/DEBIAN dh_gencontrol -a install -m0755 -d debian/bedtools/DEBIAN echo misc:Depends= >> debian/bedtools.substvars echo misc:Pre-Depends= >> debian/bedtools.substvars install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=ed72a9e8c987581c53f9e8dd5e39db5d003fbcee -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools chmod 0644 -- debian/bedtools/DEBIAN/control dh_md5sums -a install -m0755 -d debian/bedtools/DEBIAN cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/bedtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/bedtools .. dpkg-deb: building package 'bedtools' in '../bedtools_2.31.1+dfsg-1_arm64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/bedtools/dbgsym-root .. dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=any -O../bedtools_2.31.1+dfsg-1_arm64.buildinfo dpkg-genchanges --build=any -O../bedtools_2.31.1+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from bedtools-2.31.1+dfsg/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-11-25T17:35:23Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedtools_2.31.1+dfsg-1_arm64.changes: ------------------------------------- Format: 1.8 Date: Fri, 24 Nov 2023 12:10:46 +0100 Source: bedtools Binary: bedtools bedtools-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 2.31.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.31.1+dfsg-1) unstable; urgency=medium . * New upstream version 2.31.1+dfsg * gcc-13.patch: remove: applied upstream. Checksums-Sha1: f12e9d4418f8f2a3b6e207aaae9b238ba4403a51 10885696 bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb 5ddba7e1eac1512de450dc18e84871d65605803b 5821 bedtools_2.31.1+dfsg-1_arm64.buildinfo 635be206b7dae65e13a01b8ebea6fed919d7f5c6 586508 bedtools_2.31.1+dfsg-1_arm64.deb Checksums-Sha256: d33a4fb6d686c5c0bd0901839a057409f64ed62a73c2a55300d4cc74c010f391 10885696 bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb 6c10443eb8a33700e542c0bce9f7010916cb28f099f5acb1a43cab7ef599822c 5821 bedtools_2.31.1+dfsg-1_arm64.buildinfo 0a30dbdd01d54eb5c067959eaf79a21a2ae401eb0ce59437a35dc192fce6f6e4 586508 bedtools_2.31.1+dfsg-1_arm64.deb Files: 143a6539cc276e00883b7365e5b94c4e 10885696 debug optional bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb 55faec41abe81103cf5a992e7c0958fc 5821 science optional bedtools_2.31.1+dfsg-1_arm64.buildinfo 755003a43321b0ff67a0dcbfd70f2b77 586508 science optional bedtools_2.31.1+dfsg-1_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedtools Binary: bedtools bedtools-dbgsym Architecture: arm64 Version: 2.31.1+dfsg-1 Checksums-Md5: 143a6539cc276e00883b7365e5b94c4e 10885696 bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb 755003a43321b0ff67a0dcbfd70f2b77 586508 bedtools_2.31.1+dfsg-1_arm64.deb Checksums-Sha1: f12e9d4418f8f2a3b6e207aaae9b238ba4403a51 10885696 bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb 635be206b7dae65e13a01b8ebea6fed919d7f5c6 586508 bedtools_2.31.1+dfsg-1_arm64.deb Checksums-Sha256: d33a4fb6d686c5c0bd0901839a057409f64ed62a73c2a55300d4cc74c010f391 10885696 bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb 0a30dbdd01d54eb5c067959eaf79a21a2ae401eb0ce59437a35dc192fce6f6e4 586508 bedtools_2.31.1+dfsg-1_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 25 Nov 2023 17:35:23 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.2), bash (= 5.2.21-1), binutils (= 2.41-7), binutils-common (= 2.41-7), binutils-x86-64-linux-gnu (= 2.41-7), bsdextrautils (= 2.39.2-6), bsdutils (= 1:2.39.2-6), build-essential (= 12.10), bzip2 (= 1.0.8-5+b1), coreutils (= 9.4-2+b1), cpp (= 4:13.2.0-1), cpp-11 (= 11.4.0-5), cpp-13 (= 13.2.0-7), dash (= 0.5.12-6), debconf (= 1.5.82), debhelper (= 13.11.8), debianutils (= 5.14), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.1), dpkg-dev (= 1.22.1), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1), g++-13 (= 13.2.0-7), gcc (= 4:13.2.0-1), gcc-11 (= 11.4.0-5), gcc-11-base (= 11.4.0-5), gcc-13 (= 13.2.0-7), gcc-13-base (= 13.2.0-7), gettext (= 0.21-13+b1), gettext-base (= 0.21-13+b1), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1), hostname (= 3.23+nmu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.4.0-5), libasan8 (= 13.2.0-7), libatomic1 (= 13.2.0-7), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-7), libblkid1 (= 2.39.2-6), libbz2-1.0 (= 1.0.8-5+b1), libbz2-dev (= 1.0.8-5+b1), libc-bin (= 2.37-12), libc-dev-bin (= 2.37-12), libc6 (= 2.37-12), libc6-dev (= 2.37-12), libcap-ng0 (= 0.8.3-1+b3), libcap2 (= 1:2.66-4), libcc1-0 (= 13.2.0-7), libcom-err2 (= 1.47.0-2+b1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-7), libctf0 (= 2.41-7), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271), libdebhelper-perl (= 13.11.8), libdpkg-perl (= 1.22.1), libelf1 (= 0.190-1), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-2), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-11-dev (= 11.4.0-5), libgcc-13-dev (= 13.2.0-7), libgcc-s1 (= 13.2.0-7), libgcrypt20 (= 1.10.2-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.3.0+dfsg-2), libgomp1 (= 13.2.0-7), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.41-7), libgssapi-krb5-2 (= 1.20.1-5), libhwasan0 (= 13.2.0-7), libicu72 (= 72.1-4), libisl23 (= 0.26-3), libitm1 (= 13.2.0-7), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblsan0 (= 13.2.0-7), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.5-0.1), liblzma5 (= 5.4.5-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmount1 (= 2.39.2-6), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20231121-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-9.1), libpam-modules-bin (= 1.5.2-9.1), libpam-runtime (= 1.5.2-9.1), libpam0g (= 1.5.2-9.1), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-9), libpipeline1 (= 1.5.7-1), libpython3-stdlib (= 3.11.4-5+b1), libpython3.11-minimal (= 3.11.6-3), libpython3.11-stdlib (= 3.11.6-3), libquadmath0 (= 13.2.0-7), libreadline8 (= 8.2-2), libseccomp2 (= 2.5.4-2), libselinux1 (= 3.5-1), libsframe1 (= 2.41-7), libsmartcols1 (= 2.39.2-6), libsqlite3-0 (= 3.44.0-1), libssl3 (= 3.0.12-2), libstdc++-13-dev (= 13.2.0-7), libstdc++6 (= 13.2.0-7), libsub-override-perl (= 0.09-4), libsystemd0 (= 255~rc3-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4+20231121-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtool (= 2.4.7-7), libtsan0 (= 11.4.0-5), libtsan2 (= 13.2.0-7), libubsan1 (= 13.2.0-7), libuchardet0 (= 0.0.7-1), libudev1 (= 255~rc3-2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6), libxml2 (= 2.9.14+dfsg-1.3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.5.10-1), login (= 1:4.13+dfsg1-3), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231102-1), media-types (= 10.1.0), ncurses-base (= 6.4+20231121-1), ncurses-bin (= 6.4+20231121-1), patch (= 2.7.6-7), perl (= 5.36.0-9), perl-base (= 5.36.0-9), perl-modules-5.36 (= 5.36.0-9), po-debconf (= 1.0.21+nmu1), python3 (= 3.11.4-5+b1), python3-minimal (= 3.11.4-5+b1), python3.11 (= 3.11.6-3), python3.11-minimal (= 3.11.6-3), readline-common (= 8.2-2), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3), tar (= 1.34+dfsg-1.2), tzdata (= 2023c-10), usrmerge (= 38), util-linux (= 2.39.2-6), xz-utils (= 5.4.5-0.1), zlib1g (= 1:1.3.dfsg-3), zlib1g-dev (= 1:1.3.dfsg-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1700824246" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedtools-dbgsym_2.31.1+dfsg-1_arm64.deb --------------------------------------- new Debian package, version 2.0. size 10885696 bytes: control archive=540 bytes. 388 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bedtools-dbgsym Source: bedtools Version: 2.31.1+dfsg-1 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 10914 Depends: bedtools (= 2.31.1+dfsg-1) Section: debug Priority: optional Description: debug symbols for bedtools Build-Ids: ed72a9e8c987581c53f9e8dd5e39db5d003fbcee drwxr-xr-x root/root 0 2023-11-24 11:10 ./ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/lib/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/lib/debug/.build-id/ed/ -rw-r--r-- root/root 11164712 2023-11-24 11:10 ./usr/lib/debug/.build-id/ed/72a9e8c987581c53f9e8dd5e39db5d003fbcee.debug drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-11-24 11:10 ./usr/share/doc/bedtools-dbgsym -> bedtools bedtools_2.31.1+dfsg-1_arm64.deb -------------------------------- new Debian package, version 2.0. size 586508 bytes: control archive=2184 bytes. 917 bytes, 20 lines control 2915 bytes, 50 lines md5sums Package: bedtools Version: 2.31.1+dfsg-1 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 2006 Depends: libbz2-1.0, libc6 (>= 2.34), libgcc-s1 (>= 4.2), liblzma5 (>= 5.1.1alpha+20120614), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) Conflicts: filo Replaces: filo Provides: filo Section: science Priority: optional Homepage: https://github.com/arq5x/bedtools2 Description: suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. . The groupBy utility is distributed in the filo package. drwxr-xr-x root/root 0 2023-11-24 11:10 ./ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/bin/ -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/annotateBed -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/bamToBed -rwxr-xr-x root/root 43 2023-11-24 11:10 ./usr/bin/bamToFastq -rwxr-xr-x root/root 44 2023-11-24 11:10 ./usr/bin/bed12ToBed6 -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/bedToBam -rwxr-xr-x root/root 36 2023-11-24 11:10 ./usr/bin/bedToIgv -rwxr-xr-x root/root 43 2023-11-24 11:10 ./usr/bin/bedpeToBam -rwxr-xr-x root/root 1968496 2023-11-24 11:10 ./usr/bin/bedtools -rwxr-xr-x root/root 40 2023-11-24 11:10 ./usr/bin/closestBed -rwxr-xr-x root/root 40 2023-11-24 11:10 ./usr/bin/clusterBed -rwxr-xr-x root/root 43 2023-11-24 11:10 ./usr/bin/complementBed -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/coverageBed -rwxr-xr-x root/root 39 2023-11-24 11:10 ./usr/bin/expandCols -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/fastaFromBed -rwxr-xr-x root/root 38 2023-11-24 11:10 ./usr/bin/flankBed -rwxr-xr-x root/root 42 2023-11-24 11:10 ./usr/bin/genomeCoverageBed -rwxr-xr-x root/root 40 2023-11-24 11:10 ./usr/bin/getOverlap -rwxr-xr-x root/root 40 2023-11-24 11:10 ./usr/bin/groupBy -rwxr-xr-x root/root 42 2023-11-24 11:10 ./usr/bin/intersectBed -rwxr-xr-x root/root 38 2023-11-24 11:10 ./usr/bin/linksBed -rwxr-xr-x root/root 36 2023-11-24 11:10 ./usr/bin/mapBed -rwxr-xr-x root/root 42 2023-11-24 11:10 ./usr/bin/maskFastaFromBed -rwxr-xr-x root/root 38 2023-11-24 11:10 ./usr/bin/mergeBed -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/multiBamCov -rwxr-xr-x root/root 43 2023-11-24 11:10 ./usr/bin/multiIntersectBed -rwxr-xr-x root/root 36 2023-11-24 11:10 ./usr/bin/nucBed -rwxr-xr-x root/root 42 2023-11-24 11:10 ./usr/bin/pairToBed -rwxr-xr-x root/root 43 2023-11-24 11:10 ./usr/bin/pairToPair -rwxr-xr-x root/root 39 2023-11-24 11:10 ./usr/bin/randomBed -rwxr-xr-x root/root 38 2023-11-24 11:10 ./usr/bin/shiftBed -rwxr-xr-x root/root 40 2023-11-24 11:10 ./usr/bin/shuffleBed -rwxr-xr-x root/root 37 2023-11-24 11:10 ./usr/bin/slopBed -rwxr-xr-x root/root 37 2023-11-24 11:10 ./usr/bin/sortBed -rwxr-xr-x root/root 41 2023-11-24 11:10 ./usr/bin/subtractBed -rwxr-xr-x root/root 36 2023-11-24 11:10 ./usr/bin/tagBam -rwxr-xr-x root/root 42 2023-11-24 11:10 ./usr/bin/unionBedGraphs -rwxr-xr-x root/root 39 2023-11-24 11:10 ./usr/bin/windowBed -rwxr-xr-x root/root 44 2023-11-24 11:10 ./usr/bin/windowMaker drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/bash-completion/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/bash-completion/completions/ -rw-r--r-- root/root 638 2023-06-23 19:59 ./usr/share/bash-completion/completions/bedtools drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/bedtools/ drwxr-xr-x root/root 0 2023-11-07 23:23 ./usr/share/bedtools/genomes/ -rw-r--r-- root/root 868 2023-11-07 23:23 ./usr/share/bedtools/genomes/human.hg18.genome -rw-r--r-- root/root 1984 2023-11-07 23:23 ./usr/share/bedtools/genomes/human.hg19.genome -rw-r--r-- root/root 11684 2023-11-07 23:23 ./usr/share/bedtools/genomes/human.hg38.genome -rw-r--r-- root/root 1417 2023-11-07 23:23 ./usr/share/bedtools/genomes/mouse.mm10.genome -rw-r--r-- root/root 577 2023-11-07 23:23 ./usr/share/bedtools/genomes/mouse.mm8.genome -rw-r--r-- root/root 596 2023-11-07 23:23 ./usr/share/bedtools/genomes/mouse.mm9.genome drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-11-24 11:10 ./usr/share/doc/bedtools/ -rw-r--r-- root/root 3328 2023-11-07 23:23 ./usr/share/doc/bedtools/README.md -rw-r--r-- root/root 278 2023-06-23 19:59 ./usr/share/doc/bedtools/README.test -rw-r--r-- root/root 2553 2023-11-24 11:10 ./usr/share/doc/bedtools/changelog.Debian.gz -rw-r--r-- root/root 5451 2023-06-23 20:13 ./usr/share/doc/bedtools/copyright -rw-r--r-- root/root 628 2023-06-23 19:59 ./usr/share/doc/bedtools/run-unit-test lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1346 B] Get:5 copy:/<>/apt_archive ./ Packages [1425 B] Fetched 3386 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:arm64 t1utils unzip 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 12.7 MB of archives. After this operation, 49.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.12-2 [1419 kB] Get:4 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:5 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:6 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB] Get:7 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get:8 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get:9 http://localhost:3142/debian sid/main amd64 iso-codes all 4.15.0-1 [2906 kB] Get:10 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:11 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:12 http://localhost:3142/debian sid/main amd64 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libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:23 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:24 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:25 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.21-1 [95.6 kB] Get:26 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:27 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.60-1 [219 kB] Get:28 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:29 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:30 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:32 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:33 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libdata-dpath-perl all 0.59-1 [43.6 kB] Get:44 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:45 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:46 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:47 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:49 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:51 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:52 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:53 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:54 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:55 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:56 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:58 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:59 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:60 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:61 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:62 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:63 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:64 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:65 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:69 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:70 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:71 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.084-1 [216 kB] Get:72 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:73 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.11-1 [10.5 kB] Get:74 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:75 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.72-1 [187 kB] Get:76 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:77 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:78 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:79 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:80 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:81 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:82 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:83 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-6 [37.8 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:86 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:87 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:88 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:89 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:91 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:92 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:93 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:94 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:95 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:96 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1 [12.5 kB] Get:97 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:98 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:99 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:100 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:101 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1 [43.0 kB] Get:102 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:103 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1 [99.5 kB] Get:104 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1 [102 kB] Get:105 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:106 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.38-1 [60.0 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-1 [28.8 kB] Get:108 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:109 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:110 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB] Get:111 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:113 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:114 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:115 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:116 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:117 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB] Get:118 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-6 [63.1 kB] Get:119 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:120 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:121 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:122 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:123 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.7 MB in 0s (75.1 MB/s) Selecting previously unselected package netbase. (Reading database ... 21624 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.0.12-2_amd64.deb ... Unpacking openssl (3.0.12-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../003-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../004-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../005-gpgconf_2.2.40-1.1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package gpg. 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Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1) ... Setting up libsyntax-keyword-try-perl (0.29-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.636-1) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.40-1.1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.12-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.21-1) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libio-socket-ssl-perl (2.084-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.60-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.72-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.11-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.37-12) ... Processing triggers for man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 276172 Build-Time: 236 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 15 Job: bedtools_2.31.1+dfsg-1 Lintian: pass Machine Architecture: amd64 Package: bedtools Package-Time: 264 Source-Version: 2.31.1+dfsg-1 Space: 276172 Status: successful Version: 2.31.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2023-11-25T17:35:23Z Build needed 00:04:24, 276172k disk space