Diff of the two buildlogs:
--
--- b1/build.log 2025-03-16 15:25:33.860804918 +0000
+++ b2/build.log 2025-03-16 15:27:57.782331100 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Sun Mar 16 03:22:01 -12 2025
-I: pbuilder-time-stamp: 1742138521
+I: Current time: Sun Apr 19 11:48:36 +14 2026
+I: pbuilder-time-stamp: 1776548916
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
@@ -32,51 +32,83 @@
dpkg-source: info: applying cmakelists-fixups.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/193205/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/D01_modify_environment starting
+debug: Running on infom02-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Apr 18 21:48 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='amd64'
- DEBIAN_FRONTEND='noninteractive'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
- DISTRIBUTION='trixie'
- HOME='/root'
- HOST_ARCH='amd64'
+ DIRSTACK=()
+ DISTRIBUTION=trixie
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='54241445f21240d0b4f5758ed609f6ff'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- MAIL='/var/mail/root'
- OPTIND='1'
- PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
- PBCURRENTCOMMANDLINEOPERATION='build'
- PBUILDER_OPERATION='build'
- PBUILDER_PKGDATADIR='/usr/share/pbuilder'
- PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
- PBUILDER_SYSCONFDIR='/etc'
- PPID='193205'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=8b61ae09c9864dff9b80d1ae0984675a
+ LANG=C
+ LANGUAGE=et_EE:et
+ LC_ALL=C
+ MACHTYPE=x86_64-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=1706889
PS4='+ '
- PWD='/'
- SHELL='/bin/bash'
- SHLVL='2'
- SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qNdUVg5w/pbuilderrc_q54z --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qNdUVg5w/b1 --logfile b1/build.log libvcflib_1.0.12+dfsg-1.dsc'
- SUDO_GID='109'
- SUDO_UID='104'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qNdUVg5w/pbuilderrc_3lJd --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qNdUVg5w/b2 --logfile b2/build.log libvcflib_1.0.12+dfsg-1.dsc'
+ SUDO_GID=109
+ SUDO_UID=104
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
I: uname -a
- Linux infom01-amd64 6.1.0-32-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/193205/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -288,7 +320,7 @@
Get: 142 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-2 [26.1 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.6-2 [215 kB]
-Fetched 72.7 MB in 2s (44.9 MB/s)
+Fetched 72.7 MB in 3s (27.9 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:amd64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19803 files and directories currently installed.)
@@ -767,8 +799,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Sun Mar 16 15:24:09 UTC 2025.
-Universal Time is now: Sun Mar 16 15:24:09 UTC 2025.
+Local time is now: Sat Apr 18 21:49:26 UTC 2026.
+Universal Time is now: Sat Apr 18 21:49:26 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up autotools-dev (20220109.1) ...
@@ -891,7 +923,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/libvcflib-1.0.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libvcflib_1.0.12+dfsg-1_source.changes
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/libvcflib-1.0.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libvcflib_1.0.12+dfsg-1_source.changes
dpkg-buildpackage: info: source package libvcflib
dpkg-buildpackage: info: source version 1.0.12+dfsg-1
dpkg-buildpackage: info: source distribution unstable
@@ -983,8 +1019,8 @@
-- Using included tabixpp
-- WFA using include /usr/include/wfa2lib
Pandoc needs to be installed to generate the man pages
--- Configuring done (3.0s)
--- Generating done (0.3s)
+-- Configuring done (3.6s)
+-- Generating done (0.4s)
CMake Warning:
Manually-specified variables were not used by the project:
@@ -1012,28 +1048,28 @@
make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o
-[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o
-[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/canonicalize.cpp.o
-[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/legacy.cpp.o -MF CMakeFiles/vcflib.dir/src/legacy.cpp.o.d -o CMakeFiles/vcflib.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/canonicalize.cpp.o -MF CMakeFiles/vcflib.dir/src/canonicalize.cpp.o.d -o CMakeFiles/vcflib.dir/src/canonicalize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/canonicalize.cpp
-[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o
-[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o
-[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/var.cpp
-[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o
-[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o
-[ 5%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/cdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/cdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/cdflib.cpp
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-[ 6%] Building CXX object CMakeFiles/vcflib.dir/src/murmur3.cpp.o
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/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar/progress.c: In function 'print_timedelta':
/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar/progress.c:79:28: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds);
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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-[ 22%] Linking CXX executable bFst
-/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfecho.dir/link.d CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/smoother.cpp
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-[ 22%] Linking CXX executable popStats
-[ 22%] Built target vcfecho
-/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1
+[ 23%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfld.cpp
+[ 23%] Built target vcfecho
make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 23%] Linking CXX executable wcFst
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[ 24%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -MF CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o.d -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/plotHaps.cpp
-[ 24%] Linking CXX executable pVst
-/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1
-[ 24%] Linking CXX executable genotypeSummary
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-[ 24%] Linking CXX executable iHS
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 24%] Built target wcFst
+[ 24%] Built target bFst
make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake "--color="
-[ 24%] Built target popStats
make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake "--color="
@@ -1287,11 +1323,9 @@
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[ 25%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 25%] Built target smoother
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make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake "--color="
@@ -1300,48 +1334,46 @@
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 26%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/permuteSmooth.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bFst.dir/link.d CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/genotypeSummary.dir/link.d CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -o genotypeSummary -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 26%] Built target bFst
+[ 26%] Built target genotypeSummary
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hapLrt.dir/link.d CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake "--color="
+[ 26%] Built target hapLrt
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 27%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -MF CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o.d -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/normalize-iHS.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/genotypeSummary.dir/link.d CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -o genotypeSummary -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 27%] Built target genotypeSummary
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pVst.dir/link.d CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 28%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/meltEHH.cpp
-[ 29%] Linking CXX executable vcfld
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1
-[ 29%] Linking CXX executable plotHaps
-/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/iHS.dir/link.d CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 29%] Built target iHS
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake "--color="
+[ 27%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -MF CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o.d -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/normalize-iHS.cpp
+[ 27%] Built target pVst
make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnullgenofields.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 29%] Linking CXX executable permuteGPAT++
-/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1
-[ 29%] Building CXX object CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o
+[ 28%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o
+[ 28%] Building CXX object CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/meltEHH.cpp
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -MF CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o.d -o CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfnullgenofields.cpp
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 29%] Built target pVst
+[ 28%] Linking CXX executable pFst
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+[ 29%] Built target iHS
make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake "--color="
@@ -1350,9 +1382,11 @@
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 30%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfaltcount.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sequenceDiversity.dir/link.d CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+[ 30%] Linking CXX executable permuteGPAT++
+/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smoother.dir/link.d CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 30%] Built target sequenceDiversity
+[ 30%] Built target smoother
make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake "--color="
@@ -1361,228 +1395,234 @@
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 30%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -MF CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o.d -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfhetcount.cpp
+[ 30%] Linking CXX executable plotHaps
+/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sequenceDiversity.dir/link.d CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 30%] Linking CXX executable normalize-iHS
/usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/permuteGPAT++.dir/link.d CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 30%] Built target permuteGPAT++
+[ 30%] Built target sequenceDiversity
make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake "--color="
-[ 30%] Linking CXX executable permuteSmooth
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make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 30%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfhethomratio.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hapLrt.dir/link.d CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pFst.dir/link.d CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/permuteGPAT++.dir/link.d CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 30%] Built target hapLrt
+[ 30%] Linking CXX executable permuteSmooth
+/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1
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make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend
-[ 30%] Linking CXX executable abba-baba
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake "--color="
-[ 30%] Built target pFst
-make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 31%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcffilter.cpp
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 32%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o
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/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2tsv.cpp
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-[ 32%] Built target normalize-iHS
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend
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cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color="
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+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake "--color="
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-[ 32%] Built target permuteSmooth
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-[ 33%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 37%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -MF CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o.d -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremovesamples.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/abba-baba.dir/link.d "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 37%] Linking CXX executable vcf2tsv
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1
[ 37%] Built target abba-baba
-make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend
+make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build
+make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake "--color="
-[ 37%] Linking CXX executable vcffilter
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 37%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepsamples.cpp
-[ 38%] Linking CXX executable vcfgenotypes
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1
-[ 38%] Linking CXX executable vcfcommonsamples
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-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnullgenofields.dir/link.d CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -o vcfnullgenofields -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 38%] Built target vcfnullgenofields
-make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake "--color="
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 37%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -MF CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o.d -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremovesamples.cpp
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 38%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o
+[ 37%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepsamples.cpp
+[ 37%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -MF CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o.d -o CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsamplenames.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfaltcount.dir/link.d CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+[ 37%] Linking CXX executable vcffilter
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnullgenofields.dir/link.d CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -o vcfnullgenofields -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 38%] Built target vcfaltcount
+[ 37%] Built target vcfnullgenofields
make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 39%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o
+[ 38%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -MF CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o.d -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenotypecompare.cpp
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+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhetcount.dir/link.d CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 39%] Built target vcfhethomratio
+[ 38%] Built target vcfhetcount
make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 39%] Linking CXX executable vcfannotategenotypes
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1
-[ 40%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhetcount.dir/link.d CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+[ 39%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -MF CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o.d -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcffixup.cpp
+[ 40%] Linking CXX executable vcfgenotypes
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1
+[ 40%] Linking CXX executable vcf2tsv
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1
+[ 41%] Linking CXX executable vcfsamplenames
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1
+[ 41%] Linking CXX executable vcfcommonsamples
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhethomratio.dir/link.d CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 40%] Built target vcfhetcount
+[ 41%] Built target vcfhethomratio
make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 41%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o
+[ 42%] Linking CXX executable vcfkeepsamples
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1
+[ 43%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -MF CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o.d -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfclassify.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcommonsamples.dir/link.d CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/meltEHH.dir/link.d CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 41%] Built target vcfcommonsamples
+[ 43%] Built target meltEHH
make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake "--color="
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-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 41%] Built target vcfgenotypes
+[ 44%] Linking CXX executable vcfremovesamples
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1
+[ 44%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsamplediff.cpp
+[ 44%] Linking CXX executable vcfannotategenotypes
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 44%] Built target vcfsamplenames
make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color="
-[ 41%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsamplediff.cpp
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build
-[ 42%] Linking CXX executable vcfremovesamples
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 42%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o
+[ 44%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremoveaberrantgenotypes.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2tsv.dir/link.d CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
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+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepsamples.dir/link.d CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgenotypes.dir/link.d CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 42%] Built target vcf2tsv
+[ 44%] Built target vcfgenotypes
+[ 44%] Built target vcfkeepsamples
make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend
+make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color="
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color="
-[ 43%] Linking CXX executable vcfkeepsamples
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build
+make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 43%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfrandom.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/meltEHH.dir/link.d CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcommonsamples.dir/link.d CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 43%] Built target meltEHH
-make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color="
-[ 44%] Linking CXX executable vcfsamplenames
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build
+make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 45%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o
+[ 45%] Linking CXX executable vcffixup
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -MF CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o.d -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfflatten.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcffilter.dir/link.d CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 45%] Built target vcffilter
+[ 45%] Built target vcfcommonsamples
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1
make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepsamples.dir/link.d CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 45%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfrandom.cpp
[ 45%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfprimers.cpp
-[ 45%] Built target vcfkeepsamples
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcffilter.dir/link.d CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 45%] Built target vcffilter
make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake "--color="
@@ -1593,270 +1633,266 @@
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfnumalt.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfremovesamples.dir/link.d CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplenames.dir/link.d CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 45%] Built target vcfremovesamples
make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend
-[ 45%] Built target vcfsamplenames
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake "--color="
-make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build
[ 45%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -MF CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o.d -o CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfintersect.cpp
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake "--color="
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 45%] Linking CXX executable vcfgenotypecompare
[ 46%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -MF CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o.d -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfannotate.cpp
-[ 46%] Linking CXX executable vcfclassify
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-[ 46%] Linking CXX executable vcffixup
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[ 47%] Linking CXX executable vcfremoveaberrantgenotypes
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1
-[ 48%] Linking CXX executable vcfsamplediff
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1
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[ 49%] Linking CXX executable vcfrandom
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfclassify.dir/link.d CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 49%] Built target vcfclassify
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make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake "--color="
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 49%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o
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/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfoverlay.cpp
-[ 50%] Linking CXX executable vcfprimers
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[ 51%] Linking CXX executable vcfnumalt
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+[ 51%] Built target vcfgenotypecompare
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 51%] Built target vcffixup
make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake "--color="
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 52%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfaddinfo.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfremoveaberrantgenotypes.dir/link.d CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 52%] Built target vcfremoveaberrantgenotypes
-make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake "--color="
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build
-[ 52%] Built target vcfannotategenotypes
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 52%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepinfo.cpp
+[ 52%] Linking CXX executable vcfflatten
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfprimers.dir/link.d CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 52%] Built target vcfprimers
make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color="
-[ 52%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepinfo.cpp
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfremoveaberrantgenotypes.dir/link.d CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 52%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepgeno.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplediff.dir/link.d CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 52%] Built target vcfsamplediff
+[ 52%] Built target vcfremoveaberrantgenotypes
make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build
+[ 52%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepgeno.cpp
[ 53%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfafpath.cpp
-[ 53%] Linking CXX executable vcfannotate
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfprimers.dir/link.d CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfannotategenotypes.dir/link.d CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 53%] Built target vcfprimers
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnumalt.dir/link.d CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+[ 53%] Built target vcfannotategenotypes
make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color="
-[ 53%] Built target vcfnumalt
-make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color="
[ 54%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcountalleles.cpp
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfrandom.dir/link.d CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 54%] Built target vcfrandom
+make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnumalt.dir/link.d CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 54%] Built target vcfnumalt
[ 54%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcflength.dir/src/vcflength.cpp.o -MF CMakeFiles/vcflength.dir/src/vcflength.cpp.o.d -o CMakeFiles/vcflength.dir/src/vcflength.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcflength.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfrandom.dir/link.d CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplediff.dir/link.d CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 54%] Built target vcfrandom
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcflength.dir/src/vcflength.cpp.o -MF CMakeFiles/vcflength.dir/src/vcflength.cpp.o.d -o CMakeFiles/vcflength.dir/src/vcflength.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcflength.cpp
make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 55%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -MF CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o.d -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfdistance.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgenotypecompare.dir/link.d CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 55%] Built target vcfgenotypecompare
+[ 54%] Built target vcfsamplediff
make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build
+[ 54%] Linking CXX executable vcfannotate
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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+[ 55%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o
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[ 55%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfrandomsample.cpp
[ 56%] Linking CXX executable vcfoverlay
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1
-[ 56%] Linking CXX executable vcfaddinfo
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/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 57%] Linking CXX executable vcfintersect
-[ 57%] Built target vcfflatten
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make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake "--color="
-[ 58%] Linking CXX executable vcfkeepinfo
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 59%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o
+[ 60%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfentropy.cpp
-[ 60%] Linking CXX executable vcfkeepgeno
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1
-[ 60%] Linking CXX executable vcfcountalleles
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1
-[ 60%] Linking CXX executable vcfafpath
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1
[ 61%] Linking CXX executable vcflength
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1
-[ 61%] Linking CXX executable vcfdistance
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepinfo.dir/link.d CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 62%] Linking CXX executable vcfrandomsample
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1
+[ 62%] Linking CXX executable vcfdistance
+[ 62%] Built target vcfkeepinfo
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfaddinfo.dir/link.d CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 61%] Built target vcfaddinfo
+[ 62%] Built target vcfaddinfo
make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color="
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-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 61%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -MF CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o.d -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfglxgt.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcountalleles.dir/link.d CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 61%] Built target vcfcountalleles
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepinfo.dir/link.d CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color="
+[ 62%] Built target vcfcountalleles
make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color="
+[ 62%] Built target vcfkeepgeno
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build
make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 61%] Built target vcfkeepinfo
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake "--color="
-[ 62%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcheck.cpp
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 62%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o
+[ 62%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o
+[ 63%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -MF CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o.d -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfglxgt.cpp
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+[ 63%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfstreamsort.cpp
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 62%] Built target vcfkeepgeno
+[ 63%] Built target vcflength
make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 62%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o
+[ 63%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfuniq.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfoverlay.dir/link.d CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
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-[ 62%] Built target vcfoverlay
+[ 63%] Linking CXX executable vcfentropy
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1
+[ 63%] Built target vcfoverlay
make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color="
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-[ 62%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o
+[ 63%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -MF CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o.d -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfuniqalleles.cpp
-[ 63%] Linking CXX executable vcfrandomsample
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1
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-[ 63%] Built target vcfannotate
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfafpath.dir/link.d CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color="
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-[ 63%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o
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-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfafpath.dir/link.d CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
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+[ 63%] Built target vcfannotate
[ 63%] Built target vcfafpath
make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 64%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o
-[ 64%] Built target vcfdistance
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2fasta.cpp
make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 64%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o
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-[ 64%] Linking CXX executable vcfentropy
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+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfdistance.dir/link.d CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 64%] Built target vcflength
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 63%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o
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+[ 63%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsitesummarize.cpp
+[ 63%] Built target vcfdistance
+[ 64%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o
make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2fasta.cpp
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
@@ -1870,116 +1906,114 @@
make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake "--color="
-[ 65%] Linking CXX executable vcfcheck
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 66%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -MF CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o.d -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfevenregions.cpp
-[ 67%] Linking CXX executable vcfuniq
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1
-[ 68%] Linking CXX executable vcfglxgt
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+[ 67%] Linking CXX executable vcfglxgt
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1
-[ 69%] Linking CXX executable vcfuniqalleles
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1
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-[ 70%] Built target vcfentropy
+[ 68%] Built target vcfentropy
make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 71%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o
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/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -MF CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o.d -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcat.cpp
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcheck.dir/link.d CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 71%] Built target vcfcheck
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make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 72%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o
+[ 73%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -MF CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o.d -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenosummarize.cpp
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 72%] Built target vcfuniq
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make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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[ 74%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o
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+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglxgt.dir/link.d CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 74%] Built target vcfuniqalleles
-[ 75%] Linking CXX executable vcfremap
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfintersect.dir/link.d CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 74%] Built target vcfglxgt
make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend
+[ 74%] Linking CXX executable vcf2fasta
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color="
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 76%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o
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-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglxgt.dir/link.d CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 76%] Built target vcfglxgt
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make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 75%] Linking CXX executable vcfremap
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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[ 76%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -MF CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o.d -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfleftalign.cpp
-[ 76%] Linking CXX executable vcfevenregions
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 76%] Linking CXX executable vcfcat
-[ 76%] Built target vcfsitesummarize
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make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color="
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 77%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 77%] Built target vcfintersect
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make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend
-[ 77%] Linking CXX executable vcfgenosummarize
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake "--color="
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 78%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -MF CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o.d -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgeno2alleles.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfstreamsort.dir/link.d CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfevenregions.dir/link.d CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 78%] Built target vcfstreamsort
+[ 78%] Built target vcfevenregions
+[ 78%] Linking CXX executable vcfcat
make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
@@ -1987,176 +2021,175 @@
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 78%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfindex.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfbreakmulti.dir/link.d CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-[ 78%] Linking CXX executable vcfgenosamplenames
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfevenregions.dir/link.d CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfstreamsort.dir/link.d CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 78%] Built target vcfbreakmulti
-[ 78%] Built target vcfevenregions
+[ 78%] Linking CXX executable vcfgenosummarize
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1
+[ 78%] Built target vcfstreamsort
make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color="
-make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 79%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2dag.cpp
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfbreakmulti.dir/link.d CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 79%] Built target vcfbreakmulti
+make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend
+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 79%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o
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[ 79%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -MF CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o.d -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsample2info.cpp
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+[ 79%] Linking CXX executable vcfgenosamplenames
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 79%] Built target vcf2fasta
+[ 80%] Built target vcfcat
make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcat.dir/link.d CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 79%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o
+[ 80%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfqual2info.cpp
-[ 79%] Built target vcfcat
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2fasta.dir/link.d CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 80%] Linking CXX executable vcfgeno2alleles
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1
+[ 80%] Built target vcf2fasta
make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color="
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make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 79%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o
+[ 80%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -MF CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o.d -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfinfo2qual.cpp
-[ 80%] Linking CXX executable vcfleftalign
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1
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+[ 81%] Linking CXX executable vcfindex
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 80%] Built target vcfgenosamplenames
+[ 81%] Linking CXX executable vcfgeno2haplo
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make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build
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-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 80%] Built target vcfremap
-make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake "--color="
-[ 80%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o
+[ 81%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -MF CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o.d -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfglbound.cpp
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build
-make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 80%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 80%] Linking CXX executable vcfgeno2alleles
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-[ 80%] Built target vcfgenosummarize
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make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake "--color="
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 81%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o
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+make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 83%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -MF CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o.d -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcreatemulti.cpp
-[ 82%] Linking CXX executable vcfindex
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1
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-[ 82%] Linking CXX executable vcfgeno2haplo
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-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1
+[ 83%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -MF CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o.d -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfinfosummarize.cpp
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[ 84%] Linking CXX executable vcfqual2info
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-[ 87%] Built target vcfleftalign
+[ 84%] Built target vcfgeno2alleles
make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend
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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 88%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o
+[ 85%] Linking CXX executable vcfinfo2qual
+[ 86%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfallelicprimitives.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgeno2alleles.dir/link.d CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
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-[ 88%] Built target vcfgeno2alleles
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make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake "--color="
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 89%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o
+[ 87%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcleancomplex.cpp
-[ 89%] Linking CXX executable vcfcreatemulti
-/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1
-[ 89%] Built target vcfindex
-[ 89%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
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-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfleftalign.dir/link.d CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 89%] Built target vcfqual2info
-[ 89%] Built target vcfinfo2qual
-[ 89%] Built target vcfsample2info
+[ 87%] Built target vcfleftalign
make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake "--color="
-[ 90%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o
-[ 90%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsample2info.dir/link.d CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 90%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 87%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfparsealts.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglbound.dir/link.d CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+[ 87%] Built target vcfsample2info
+[ 88%] Building CXX object CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfqual2info.dir/link.d CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2dag.dir/link.d CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfinfo2qual.dir/link.d CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 90%] Built target vcf2dag
-[ 90%] Built target vcfglbound
+[ 88%] Built target vcfqual2info
+[ 88%] Built target vcfinfo2qual
make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 91%] Building CXX object CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o
-[ 91%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o
+[ 88%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
+[ 88%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfroc.cpp
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfinfosummarize.dir/link.d CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 91%] Built target vcfinfosummarize
+[ 88%] Built target vcf2dag
+[ 89%] Building CXX object CMakeFiles/vcfroc.dir/src/legacy.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfroc.dir/src/legacy.cpp.o -MF CMakeFiles/vcfroc.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfroc.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
+[ 90%] Linking CXX executable vcfglbound
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1
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+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
+[ 90%] Linking CXX executable vcfcreatemulti
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcombine.dir/link.d CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 91%] Linking CXX executable vcfinfosummarize
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+[ 91%] Built target vcfcombine
make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake "--color="
@@ -2165,79 +2198,82 @@
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[ 91%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfstats.cpp
-[ 92%] Building CXX object CMakeFiles/vcfstats.dir/src/legacy.cpp.o
+[ 92%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
+[ 92%] Building CXX object CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
+[ 92%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
+[ 93%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglbound.dir/link.d CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[ 93%] Built target vcfglbound
+[ 94%] Building CXX object CMakeFiles/vcfstats.dir/src/legacy.cpp.o
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/legacy.cpp.o -MF CMakeFiles/vcfstats.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfstats.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcombine.dir/link.d CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+[ 94%] Building CXX object CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 92%] Built target vcfcombine
+[ 94%] Built target vcfgeno2haplo
make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfwave.dir/DependInfo.cmake "--color="
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 92%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o
+[ 94%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o
+[ 94%] Built target vcfinfosummarize
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -MF CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o.d -o CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfwave.cpp
+[ 95%] Building CXX object CMakeFiles/vcfwave.dir/src/legacy.cpp.o
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make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend
-[ 92%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color="
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/build
make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[ 93%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp
-[ 94%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o
-/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dpyvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/python3.13 -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -fvisibility=hidden -MD -MT CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -MF CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o.d -o CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/pythonffi.cpp
-[ 95%] Building CXX object CMakeFiles/vcfwave.dir/src/legacy.cpp.o
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[ 95%] Built target vcfcreatemulti
-[ 95%] Building CXX object CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o
+[ 96%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o
+/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dpyvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/python3.13 -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -fvisibility=hidden -MD -MT CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -MF CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o.d -o CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/pythonffi.cpp
+[ 97%] Linking CXX executable vcfparsealts
+/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1
+[ 97%] Building CXX object CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o
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-[ 95%] Building CXX object CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o
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-[ 96%] Linking CXX executable vcfcleancomplex
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-[ 96%] Linking CXX executable vcfallelicprimitives
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-[ 98%] Linking CXX executable vcfwave
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+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[100%] Built target vcfcleancomplex
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfwave.dir/link.d CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o CMakeFiles/vcfwave.dir/src/legacy.cpp.o "CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o" -o vcfwave -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfallelicprimitives.dir/link.d CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o "CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o" -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[100%] Built target vcfwave
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfroc.dir/link.d CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o CMakeFiles/vcfroc.dir/src/legacy.cpp.o "CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o" -o vcfroc -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[100%] Built target vcfallelicprimitives
+[100%] Built target vcfroc
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfstats.dir/link.d CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o CMakeFiles/vcfstats.dir/src/legacy.cpp.o "CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o" -o vcfstats -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
[100%] Built target vcfstats
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfparsealts.dir/link.d CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o "CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o" -o vcfparsealts -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfallelicprimitives.dir/link.d CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o "CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o" -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
-make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
-[100%] Built target vcfparsealts
-[100%] Built target vcfallelicprimitives
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfroc.dir/link.d CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o CMakeFiles/vcfroc.dir/src/legacy.cpp.o "CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o" -o vcfroc -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfwave.dir/link.d CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o CMakeFiles/vcfwave.dir/src/legacy.cpp.o "CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o" -o vcfwave -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
+[100%] Built target vcfwave
[100%] Linking CXX shared module pyvcflib.cpython-313-x86_64-linux-gnu.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/pyvcflib.dir/link.txt --verbose=1
-[100%] Built target vcfroc
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,--dependency-file=CMakeFiles/pyvcflib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o pyvcflib.cpython-313-x86_64-linux-gnu.so CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -Wl,-rpath,"\$ORIGIN:" libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2
/usr/bin/strip /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/pyvcflib.cpython-313-x86_64-linux-gnu.so
make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
@@ -2254,27 +2290,27 @@
cd test && ctest .
Test project /build/reproducible-path/libvcflib-1.0.12+dfsg/test
Start 1: realign
-1/9 Test #1: realign .......................... Passed 0.05 sec
+1/9 Test #1: realign .......................... Passed 0.07 sec
Start 2: pyvcflib
-2/9 Test #2: pyvcflib ......................... Passed 0.05 sec
+2/9 Test #2: pyvcflib ......................... Passed 0.07 sec
Start 3: vcflib-api
-3/9 Test #3: vcflib-api ....................... Passed 0.05 sec
+3/9 Test #3: vcflib-api ....................... Passed 0.06 sec
Start 4: vcf2tsv
-4/9 Test #4: vcf2tsv .......................... Passed 0.07 sec
+4/9 Test #4: vcf2tsv .......................... Passed 0.12 sec
Start 5: vcfallelicprimitives
-5/9 Test #5: vcfallelicprimitives ............. Passed 0.82 sec
+5/9 Test #5: vcfallelicprimitives ............. Passed 0.97 sec
Start 6: vcfwave
-6/9 Test #6: vcfwave .......................... Passed 0.43 sec
+6/9 Test #6: vcfwave .......................... Passed 0.47 sec
Start 7: vcffilter
-7/9 Test #7: vcffilter ........................ Passed 0.10 sec
+7/9 Test #7: vcffilter ........................ Passed 0.16 sec
Start 8: vcfnulldotslashdot
-8/9 Test #8: vcfnulldotslashdot ............... Passed 0.06 sec
+8/9 Test #8: vcfnulldotslashdot ............... Passed 0.11 sec
Start 9: doc/vcfintersect
-9/9 Test #9: doc/vcfintersect ................. Passed 0.05 sec
+9/9 Test #9: doc/vcfintersect ................. Passed 0.08 sec
100% tests passed, 0 tests failed out of 9
-Total Test time (real) = 1.76 sec
+Total Test time (real) = 2.13 sec
cd .. && rm -f build
make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg'
create-stamp debian/debhelper-build-stamp
@@ -2515,95 +2551,95 @@
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/include/vcflib/vcf-c-api.h
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/include/vcflib/vcf-wfa.h
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfintersect.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfld.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnullgenofields.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/popStats.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandom.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcheck.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfroc.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/iHS.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcombine.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfafpath.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/wcFst.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfqual2info.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfecho.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pyvcflib.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfentropy.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfclassify.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/meltEHH.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentFst.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfindex.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfroc.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfentropy.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2dag.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcffixup.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/popStats.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfintersect.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/meltEHH.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfecho.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/bFst.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcffixup.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflib.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfprimers.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfwave.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/abba-baba.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentFst.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/smoother.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfflatten.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflength.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfafpath.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfqual2info.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfwave.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcat.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflib-api.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcombine.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/plotHaps.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstats.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentIhs.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfld.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2dag.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/hapLrt.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotate.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfclassify.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pyvcflib.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentIhs.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcheck.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandom.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstats.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfdistance.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfprimers.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnullgenofields.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflength.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniq.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/genotypeSummary.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcffilter.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pFst.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcat.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniq.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfdistance.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/abba-baba.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfglbound.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfflatten.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/plotHaps.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pFst.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremap.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/iHS.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/dumpContigsFromHeader.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/wcFst.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/permuteSmooth.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfindex.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcffilter.1
-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pVst.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotate.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1
--- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1
+-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1
make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg'
@@ -2657,10 +2693,10 @@
dh_md5sums -O--buildsystem=cmake
dh_builddeb -O--buildsystem=cmake
dpkg-deb: building package 'libvcflib2' in '../libvcflib2_1.0.12+dfsg-1_amd64.deb'.
-dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.12+dfsg-1_amd64.deb'.
dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.12+dfsg-1_amd64.deb'.
dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.12+dfsg-1_amd64.deb'.
dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.12+dfsg-1_amd64.deb'.
+dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.12+dfsg-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.12+dfsg-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../libvcflib_1.0.12+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -2668,12 +2704,14 @@
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/1706889/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/193205 and its subdirectories
-I: Current time: Sun Mar 16 03:25:33 -12 2025
-I: pbuilder-time-stamp: 1742138733
+I: removing directory /srv/workspace/pbuilder/1706889 and its subdirectories
+I: Current time: Sun Apr 19 11:50:57 +14 2026
+I: pbuilder-time-stamp: 1776549057