Diff of the two buildlogs: -- --- b1/build.log 2025-02-04 20:40:04.341709220 +0000 +++ b2/build.log 2025-02-04 20:45:33.866785309 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Mar 9 14:59:46 -12 2026 -I: pbuilder-time-stamp: 1773111586 +I: Current time: Wed Feb 5 10:40:07 +14 2025 +I: pbuilder-time-stamp: 1738701607 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,54 +33,86 @@ dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/92221/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11177/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Feb 4 20:40 /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/11177/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11177/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='3b229f2187404d0cbacff0545befb8b5' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='92221' - PS1='# ' - PS2='> ' + INVOCATION_ID=c24f780d0e9c45c2a3613d24b07f3a35 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=11177 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.NowqtDIw/pbuilderrc_1yZf --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NowqtDIw/b1 --logfile b1/build.log hisat2_2.2.1-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.NowqtDIw/pbuilderrc_Rnxx --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NowqtDIw/b2 --logfile b2/build.log hisat2_2.2.1-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/92221/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/11177/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -175,7 +207,7 @@ Get: 50 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-2 [55.8 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 pandoc-data all 3.1.11.1-3 [459 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 pandoc i386 3.1.11.1+ds-2 [37.3 MB] -Fetched 66.1 MB in 1s (66.8 MB/s) +Fetched 66.1 MB in 1s (71.0 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19792 files and directories currently installed.) @@ -361,8 +393,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Mar 10 03:00:07 UTC 2026. -Universal Time is now: Tue Mar 10 03:00:07 UTC 2026. +Local time is now: Tue Feb 4 20:40:40 UTC 2025. +Universal Time is now: Tue Feb 4 20:40:40 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -410,7 +442,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hisat2-2.2.1/ && 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 > ../hisat2_2.2.1-5_source.changes +I: user script /srv/workspace/pbuilder/11177/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/11177/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hisat2-2.2.1/ && 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 > ../hisat2_2.2.1-5_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable @@ -420,7 +456,7 @@ debian/rules clean dh clean dh_auto_clean - make -j22 clean + make -j10 clean make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \ @@ -439,7 +475,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="09 July 2024" all doc - make -j22 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc + make -j10 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/build/reproducible-path/hisat2-2.2.1' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ @@ -487,16 +523,6 @@ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from gfm.h:43, - from hisat2_build.cpp:35: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from gfm.h:43, from hisat2_repeat.cpp:36: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -506,17 +532,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from gfm.h:43, - from hgfm.h:24, - from hisat2.cpp:33: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] @@ -533,6 +548,16 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from gfm.h:43, + from hisat2_build.cpp:35: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -548,23 +573,17 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from hgfm.h:24, +In file included from gfm.h:43, + from hgfm.h:24, from hisat2.cpp:33: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -580,103 +599,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from hisat2_build.cpp:28: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29: -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:15: required from here - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ - 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ - 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ - 1071 | OFF_MASK, begin, end); - | ^~~~~~~~ -In file included from gfm.h:43, - from hgfm.h:24, - from hisat2_inspect.cpp:27: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from aligner_sw.h:76, from hisat2_repeat.cpp:37: aligner_sw_nuc.h: At global scope: @@ -684,49 +606,6 @@ 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ -multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ - 914 | off = OFF_MASK; - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ - 923 | OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ - 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( @@ -887,166 +766,38 @@ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ -gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: -gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ - 1039 | initFromVector( - | ~~~~~~~~~~~~~~~~~~~~^ - 1040 | s, - | ~~ - 1041 | snpfile, - | ~~~~~~~~ - 1042 | htfile, - | ~~~~~~~ - 1043 | ssfile, - | ~~~~~~~ - 1044 | exonfile, - | ~~~~~~~~~ - 1045 | svfile, - | ~~~~~~~ - 1046 | repeatfile, - | ~~~~~~~~~~~ - 1047 | is, - | ~~~ - 1048 | szs, - | ~~~~ - 1049 | sztot, - | ~~~~~~ - 1050 | refparams, - | ~~~~~~~~~~ - 1051 | fout1, - | ~~~~~~ - 1052 | fout2, - | ~~~~~~ - 1053 | outfile, - | ~~~~~~~~ - 1054 | useBlockwise, - | ~~~~~~~~~~~~~ - 1055 | bmax, - | ~~~~~ - 1056 | bmaxSqrtMult, - | ~~~~~~~~~~~~~ - 1057 | bmaxDivN, - | ~~~~~~~~~ - 1058 | dcv, - | ~~~~ - 1059 | parent_szs, - | ~~~~~~~~~~~ - 1060 | parent_refnames, - | ~~~~~~~~~~~~~~~~ - 1061 | seed, - | ~~~~~ - 1062 | verbose); - | ~~~~~~~~ -hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ - 1989 | _in6(NULL) - | ^ -hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ - 535 | gfm = new HGFM( - | ^~~~~~~~~~~~~~~~~~~~~ - 536 | s, - | ~~ - 537 | packed, - | ~~~~~~~ - 538 | 1, // TODO: maybe not? - | ~~~~~~~~~~~~~~~~~~~~~~~ - 539 | lineRate, - | ~~~~~~~~~ - 540 | offRate, // suffix-array sampling rate - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 541 | ftabChars, // number of chars in initial arrow-pair calc - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 542 | localOffRate, - | ~~~~~~~~~~~~~ - 543 | localFtabChars, - | ~~~~~~~~~~~~~~~ - 544 | nthreads, - | ~~~~~~~~~ - 545 | snpfile, - | ~~~~~~~~ - 546 | htfile, - | ~~~~~~~ - 547 | ssfile, - | ~~~~~~~ - 548 | exonfile, - | ~~~~~~~~~ - 549 | svfile, - | ~~~~~~~ - 550 | repeatfile, - | ~~~~~~~~~~~ - 551 | outfile, // basename for .?.ht2 files - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 552 | reverse == 0, // fw - | ~~~~~~~~~~~~~~~~~~~ - 553 | !entireSA, // useBlockwise - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 554 | bmax, // block size for blockwise SA builder - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 556 | bmaxDivN, // block size as divisor of len - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 557 | noDc? 0 : dcv,// difference-cover period - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 558 | is, // list of input streams - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 559 | szs, // list of reference sizes - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 561 | refparams, // reference read-in parameters - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 562 | localindex, // create local indexes? - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 563 | parent_szs, // parent szs - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 564 | parent_refnames, // parent refence names - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 565 | seed, // pseudo-random number generator seed - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 566 | -1, // override offRate - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 567 | verbose, // be talkative - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 569 | sanityCheck); // verify results and internal consistency - | ~~~~~~~~~~~~ -hisat2_build.cpp:786:39: required from here - 786 | driver >(infile, - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ - 787 | infiles, - | ~~~~~~~~ - 788 | snp_fname, - | ~~~~~~~~~~ - 789 | ht_fname, - | ~~~~~~~~~ - 790 | ss_fname, - | ~~~~~~~~~ - 791 | exon_fname, - | ~~~~~~~~~~~ - 792 | sv_fname, - | ~~~~~~~~~ - 793 | dummy_fname, - | ~~~~~~~~~~~~ - 794 | outfile, - | ~~~~~~~~ - 795 | false, - | ~~~~~~ - 796 | REF_READ_FORWARD, - | ~~~~~~~~~~~~~~~~~ - 797 | true, // create local indexes - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 798 | NULL, // no parent szs - | ~~~~~~~~~~~~~~~~~~~~~~ - 799 | NULL, // no parent refnames - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | &parent_szs, // get parent szs - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | &parent_refnames); // get parent refnames - | ~~~~~~~~~~~~~~~~~ -gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] - 2167 | index_t template_len = 0; - | ^~~~~~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ +In file included from gfm.h:43, + from hgfm.h:24, + from hisat2_inspect.cpp:27: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] @@ -1055,9 +806,23 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -gfm.h:2342:106: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 2342 | std::numeric_limits::max(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from hgfm.h:24, + from hisat2.cpp:33: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] @@ -1096,6 +861,57 @@ multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ds.h:32, + from sequence_io.h:28, + from hisat2_build.cpp:28: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29: +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:15: required from here + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ + 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ + 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); @@ -1213,26 +1029,6 @@ 813 | sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from aligner_sw.h:76, - from aligner_sw_driver.h:86, - from hi_aligner.h:42, - from spliced_aligner.h:23, - from hisat2.cpp:46: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -In file included from aligner_sw.h:76, - from aligner_sw_driver.h:86, - from hi_aligner.h:42, - from spliced_aligner.h:23, - from hisat2.cpp:46: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ 447 | mkeyQSortSufDcU8(t, host, len, s, slen, *_dc.get(), 4, @@ -1281,135 +1077,26 @@ multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’: -blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ - 1098 | this->qsort(bucket); - | ~~~~~~^~~~~ -blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ - 297 | nextBlock((int)_cur); - | ^~~~~~~~~ -hgfm.h:1843:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ - 1843 | tParam.sa.push_back(bsa.nextSuffix()); - | ~~~~~~~~~~~~~~^~ -hgfm.h:2211:30: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ - 2211 | threads[t] = new tthread::thread(gbwt_worker, (void*)&tParams.back()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ - 535 | gfm = new HGFM( - | ^~~~~~~~~~~~~~~~~~~~~ - 536 | s, - | ~~ - 537 | packed, - | ~~~~~~~ - 538 | 1, // TODO: maybe not? - | ~~~~~~~~~~~~~~~~~~~~~~~ - 539 | lineRate, - | ~~~~~~~~~ - 540 | offRate, // suffix-array sampling rate - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 541 | ftabChars, // number of chars in initial arrow-pair calc - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 542 | localOffRate, - | ~~~~~~~~~~~~~ - 543 | localFtabChars, - | ~~~~~~~~~~~~~~~ - 544 | nthreads, - | ~~~~~~~~~ - 545 | snpfile, - | ~~~~~~~~ - 546 | htfile, - | ~~~~~~~ - 547 | ssfile, - | ~~~~~~~ - 548 | exonfile, - | ~~~~~~~~~ - 549 | svfile, - | ~~~~~~~ - 550 | repeatfile, - | ~~~~~~~~~~~ - 551 | outfile, // basename for .?.ht2 files - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 552 | reverse == 0, // fw - | ~~~~~~~~~~~~~~~~~~~ - 553 | !entireSA, // useBlockwise - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 554 | bmax, // block size for blockwise SA builder - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 556 | bmaxDivN, // block size as divisor of len - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 557 | noDc? 0 : dcv,// difference-cover period - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 558 | is, // list of input streams - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 559 | szs, // list of reference sizes - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 561 | refparams, // reference read-in parameters - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 562 | localindex, // create local indexes? - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 563 | parent_szs, // parent szs - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 564 | parent_refnames, // parent refence names - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 565 | seed, // pseudo-random number generator seed - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 566 | -1, // override offRate - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 567 | verbose, // be talkative - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 569 | sanityCheck); // verify results and internal consistency - | ~~~~~~~~~~~~ -hisat2_build.cpp:786:39: required from here - 786 | driver >(infile, - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ - 787 | infiles, - | ~~~~~~~~ - 788 | snp_fname, - | ~~~~~~~~~~ - 789 | ht_fname, - | ~~~~~~~~~ - 790 | ss_fname, - | ~~~~~~~~~ - 791 | exon_fname, - | ~~~~~~~~~~~ - 792 | sv_fname, - | ~~~~~~~~~ - 793 | dummy_fname, - | ~~~~~~~~~~~~ - 794 | outfile, - | ~~~~~~~~ - 795 | false, - | ~~~~~~ - 796 | REF_READ_FORWARD, - | ~~~~~~~~~~~~~~~~~ - 797 | true, // create local indexes - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 798 | NULL, // no parent szs - | ~~~~~~~~~~~~~~~~~~~~~~ - 799 | NULL, // no parent refnames - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | &parent_szs, // get parent szs - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | &parent_refnames); // get parent refnames - | ~~~~~~~~~~~~~~~~~ -blockwise_sa.h:453:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 453 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 454 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:453:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ +multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ + 1071 | OFF_MASK, begin, end); + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = SString]’ 772 | mkeyQSortSuf2(t, sPrimeArr, sPrimeSz, sPrimeOrderArr, 4, @@ -1434,12 +1121,6 @@ multikey_qsort.h:661:31: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 661 | sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); @@ -1554,6 +1235,43 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ + 914 | off = OFF_MASK; + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ + 923 | OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ + 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: @@ -1565,6 +1283,175 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: +gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ + 1039 | initFromVector( + | ~~~~~~~~~~~~~~~~~~~~^ + 1040 | s, + | ~~ + 1041 | snpfile, + | ~~~~~~~~ + 1042 | htfile, + | ~~~~~~~ + 1043 | ssfile, + | ~~~~~~~ + 1044 | exonfile, + | ~~~~~~~~~ + 1045 | svfile, + | ~~~~~~~ + 1046 | repeatfile, + | ~~~~~~~~~~~ + 1047 | is, + | ~~~ + 1048 | szs, + | ~~~~ + 1049 | sztot, + | ~~~~~~ + 1050 | refparams, + | ~~~~~~~~~~ + 1051 | fout1, + | ~~~~~~ + 1052 | fout2, + | ~~~~~~ + 1053 | outfile, + | ~~~~~~~~ + 1054 | useBlockwise, + | ~~~~~~~~~~~~~ + 1055 | bmax, + | ~~~~~ + 1056 | bmaxSqrtMult, + | ~~~~~~~~~~~~~ + 1057 | bmaxDivN, + | ~~~~~~~~~ + 1058 | dcv, + | ~~~~ + 1059 | parent_szs, + | ~~~~~~~~~~~ + 1060 | parent_refnames, + | ~~~~~~~~~~~~~~~~ + 1061 | seed, + | ~~~~~ + 1062 | verbose); + | ~~~~~~~~ +hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ + 1989 | _in6(NULL) + | ^ +hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ + 535 | gfm = new HGFM( + | ^~~~~~~~~~~~~~~~~~~~~ + 536 | s, + | ~~ + 537 | packed, + | ~~~~~~~ + 538 | 1, // TODO: maybe not? + | ~~~~~~~~~~~~~~~~~~~~~~~ + 539 | lineRate, + | ~~~~~~~~~ + 540 | offRate, // suffix-array sampling rate + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 541 | ftabChars, // number of chars in initial arrow-pair calc + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 542 | localOffRate, + | ~~~~~~~~~~~~~ + 543 | localFtabChars, + | ~~~~~~~~~~~~~~~ + 544 | nthreads, + | ~~~~~~~~~ + 545 | snpfile, + | ~~~~~~~~ + 546 | htfile, + | ~~~~~~~ + 547 | ssfile, + | ~~~~~~~ + 548 | exonfile, + | ~~~~~~~~~ + 549 | svfile, + | ~~~~~~~ + 550 | repeatfile, + | ~~~~~~~~~~~ + 551 | outfile, // basename for .?.ht2 files + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 552 | reverse == 0, // fw + | ~~~~~~~~~~~~~~~~~~~ + 553 | !entireSA, // useBlockwise + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 554 | bmax, // block size for blockwise SA builder + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 556 | bmaxDivN, // block size as divisor of len + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 557 | noDc? 0 : dcv,// difference-cover period + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 558 | is, // list of input streams + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 559 | szs, // list of reference sizes + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 561 | refparams, // reference read-in parameters + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 562 | localindex, // create local indexes? + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 563 | parent_szs, // parent szs + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 564 | parent_refnames, // parent refence names + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 565 | seed, // pseudo-random number generator seed + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 566 | -1, // override offRate + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 567 | verbose, // be talkative + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 569 | sanityCheck); // verify results and internal consistency + | ~~~~~~~~~~~~ +hisat2_build.cpp:786:39: required from here + 786 | driver >(infile, + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ + 787 | infiles, + | ~~~~~~~~ + 788 | snp_fname, + | ~~~~~~~~~~ + 789 | ht_fname, + | ~~~~~~~~~ + 790 | ss_fname, + | ~~~~~~~~~ + 791 | exon_fname, + | ~~~~~~~~~~~ + 792 | sv_fname, + | ~~~~~~~~~ + 793 | dummy_fname, + | ~~~~~~~~~~~~ + 794 | outfile, + | ~~~~~~~~ + 795 | false, + | ~~~~~~ + 796 | REF_READ_FORWARD, + | ~~~~~~~~~~~~~~~~~ + 797 | true, // create local indexes + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 798 | NULL, // no parent szs + | ~~~~~~~~~~~~~~~~~~~~~~ + 799 | NULL, // no parent refnames + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | &parent_szs, // get parent szs + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | &parent_refnames); // get parent refnames + | ~~~~~~~~~~~~~~~~~ +gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] + 2167 | index_t template_len = 0; + | ^~~~~~~~~~~~ +gfm.h:2342:106: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 2342 | std::numeric_limits::max(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -1580,9 +1467,165 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ +In file included from aligner_sw.h:76, + from aligner_sw_driver.h:86, + from hi_aligner.h:42, + from spliced_aligner.h:23, + from hisat2.cpp:46: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ +blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’: +blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ + 1098 | this->qsort(bucket); + | ~~~~~~^~~~~ +blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ + 297 | nextBlock((int)_cur); + | ^~~~~~~~~ +hgfm.h:1843:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ + 1843 | tParam.sa.push_back(bsa.nextSuffix()); + | ~~~~~~~~~~~~~~^~ +hgfm.h:2211:30: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ + 2211 | threads[t] = new tthread::thread(gbwt_worker, (void*)&tParams.back()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ + 535 | gfm = new HGFM( + | ^~~~~~~~~~~~~~~~~~~~~ + 536 | s, + | ~~ + 537 | packed, + | ~~~~~~~ + 538 | 1, // TODO: maybe not? + | ~~~~~~~~~~~~~~~~~~~~~~~ + 539 | lineRate, + | ~~~~~~~~~ + 540 | offRate, // suffix-array sampling rate + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 541 | ftabChars, // number of chars in initial arrow-pair calc + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 542 | localOffRate, + | ~~~~~~~~~~~~~ + 543 | localFtabChars, + | ~~~~~~~~~~~~~~~ + 544 | nthreads, + | ~~~~~~~~~ + 545 | snpfile, + | ~~~~~~~~ + 546 | htfile, + | ~~~~~~~ + 547 | ssfile, + | ~~~~~~~ + 548 | exonfile, + | ~~~~~~~~~ + 549 | svfile, + | ~~~~~~~ + 550 | repeatfile, + | ~~~~~~~~~~~ + 551 | outfile, // basename for .?.ht2 files + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 552 | reverse == 0, // fw + | ~~~~~~~~~~~~~~~~~~~ + 553 | !entireSA, // useBlockwise + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 554 | bmax, // block size for blockwise SA builder + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 556 | bmaxDivN, // block size as divisor of len + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 557 | noDc? 0 : dcv,// difference-cover period + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 558 | is, // list of input streams + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 559 | szs, // list of reference sizes + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 561 | refparams, // reference read-in parameters + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 562 | localindex, // create local indexes? + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 563 | parent_szs, // parent szs + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 564 | parent_refnames, // parent refence names + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 565 | seed, // pseudo-random number generator seed + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 566 | -1, // override offRate + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 567 | verbose, // be talkative + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 569 | sanityCheck); // verify results and internal consistency + | ~~~~~~~~~~~~ +hisat2_build.cpp:786:39: required from here + 786 | driver >(infile, + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ + 787 | infiles, + | ~~~~~~~~ + 788 | snp_fname, + | ~~~~~~~~~~ + 789 | ht_fname, + | ~~~~~~~~~ + 790 | ss_fname, + | ~~~~~~~~~ + 791 | exon_fname, + | ~~~~~~~~~~~ + 792 | sv_fname, + | ~~~~~~~~~ + 793 | dummy_fname, + | ~~~~~~~~~~~~ + 794 | outfile, + | ~~~~~~~~ + 795 | false, + | ~~~~~~ + 796 | REF_READ_FORWARD, + | ~~~~~~~~~~~~~~~~~ + 797 | true, // create local indexes + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 798 | NULL, // no parent szs + | ~~~~~~~~~~~~~~~~~~~~~~ + 799 | NULL, // no parent refnames + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | &parent_szs, // get parent szs + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | &parent_refnames); // get parent refnames + | ~~~~~~~~~~~~~~~~~ +blockwise_sa.h:453:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 453 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 454 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:453:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from aligner_sw.h:76, + from aligner_sw_driver.h:86, + from hi_aligner.h:42, + from spliced_aligner.h:23, + from hisat2.cpp:46: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); + | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ @@ -1966,6 +2009,25 @@ multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: +hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3168 | auto_ptr ps(patsrcFact->create()); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = SString]’ 772 | mkeyQSortSuf2(t, sPrimeArr, sPrimeSz, sPrimeOrderArr, 4, @@ -2231,6 +2293,13 @@ multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: +hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 4035 | auto_ptr refs( + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, @@ -2367,20 +2436,36 @@ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ -hisat2.cpp: In function ‘void parseOptions(int, const char**)’: -hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1823 | auto_ptr presets(new PresetsV0()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void parseOptions(int, const char**)’: -hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1823 | auto_ptr presets(new PresetsV0()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ +In file included from ds.h:32, + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:15: required from here + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, @@ -2534,88 +2619,6 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: -hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3168 | auto_ptr ps(patsrcFact->create()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: -hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3168 | auto_ptr ps(patsrcFact->create()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: -hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 4035 | auto_ptr refs( - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: -hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 4035 | auto_ptr refs( - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:15: required from here - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( @@ -2685,6 +2688,13 @@ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); @@ -2821,16 +2831,13 @@ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ -gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: -hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ - 3815 | gfm.checkOrigs(os, false); - | ~~~~~~~~~~~~~~^~~~~~~~~~~ -hisat2.cpp:4351:26: required from here - 4351 | driver >("DNA", bt2index, outfile); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] - 6935 | int lastorig = -1; - | ^~~~~~~~ +hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: +hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, @@ -2851,6 +2858,48 @@ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ +hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3168 | auto_ptr ps(patsrcFact->create()); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from ds.h:32, + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:15: required from here + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ 5525 | index_t numHits = getAnchorHits(gfm, @@ -2973,6 +3022,34 @@ hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ + 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ + 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: +hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 4035 | auto_ptr refs( + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, @@ -3010,12 +3087,15 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:477:19: required from here 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3024,129 +3104,9 @@ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:15: required from here - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from aligner_seed2.h:109, - from aligner_driver.h:78, - from hi_aligner.h:41: -group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ - 1517 | st.advance( - | ~~~~~~~~~~^ - 1518 | gfmFw, - | ~~~~~~ - 1519 | ref, - | ~~~~ - 1520 | sa, - | ~~~ - 1521 | hit_, - | ~~~~~ - 1522 | (index_t)range, - | ~~~~~~~~~~~~~~~ - 1523 | false, - | ~~~~~~ - 1524 | NULL, - | ~~~~~ - 1525 | st_, - | ~~~~ - 1526 | gws, - | ~~~~ - 1527 | met, - | ~~~~ - 1528 | prm); - | ~~~~ -hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 5901 | _gws_local.advanceElement( - | ~~~~~~~~~~~~~~~~~~~~~~~~~^ - 5902 | off, - | ~~~~ - 5903 | gfm, // forward Bowtie index for walking left - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5904 | ref, // bitpair-encoded reference - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5905 | _sas_local, // SA range with offsets - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5906 | _gwstate_local, // GroupWalk state; scratch space - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5907 | wr, // put the result here - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5908 | met, // metrics - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 5909 | prm); // per-read metrics - | ~~~~ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 5664 | getGenomeCoords_local( - | ^~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 4107 | mate_found |= alignMate( - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1147 | if(new_node_bot - new_node_top < gws.map.size()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { - | ~~~~~~^~~~~~~~~~~~~~~~ -group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ + 1071 | OFF_MASK, begin, end); + | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: @@ -3254,8 +3214,8 @@ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, @@ -3314,7 +3274,7 @@ | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, @@ -3357,7 +3317,7 @@ | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, @@ -3380,7 +3340,7 @@ | ~~~~ 5702 | gpol); | ~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here @@ -3430,10 +3390,184 @@ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] +hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ -hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: +hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] + 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { + | ~~~~~^~~~~~~~ +hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 3161 | if(alignedLen == next_rdlen) return rdlen; + | ~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] + 3454 | if(best_rdoff < rdoff + rd_i) { + | ~~~~~~~~~~~^~~~~~~~~~~~~~ +multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ + 914 | off = OFF_MASK; + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ + 923 | OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ + 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: +hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ + 3815 | gfm.checkOrigs(os, false); + | ~~~~~~~~~~~~~~^~~~~~~~~~~ +hisat2.cpp:4351:26: required from here + 4351 | driver >("DNA", bt2index, outfile); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] + 6935 | int lastorig = -1; + | ^~~~~~~~ +group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ + 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ + 1453 | st_.back().init( + | ~~~~~~~~~~~~~~~^ + 1454 | gfmFw, // Bowtie index + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1455 | ref, // bitpair-encoded reference + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1456 | sa, // SA range with offsets + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1457 | st_, // EList + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1458 | hit_, // GWHit + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1459 | 0, // range 0 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1460 | false, // put resolved elements into res_? + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1461 | NULL, // put resolved elements here + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1462 | top, // GBW row at top + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1463 | bot, // GBW row at bot + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1464 | node_top, // node at top + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1465 | node_bot, // node at bot + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1466 | sa.node_iedge_count, + | ~~~~~~~~~~~~~~~~~~~~ + 1467 | 0, // # steps taken + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1468 | met); // update metrics here + | ~~~~ +hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ + 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ + 5664 | getGenomeCoords_local( + | ^~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ + 4107 | mate_found |= alignMate( + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 789 | if(new_top - top == tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 795 | if(i + 1 < tmp_zOffs.size()) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long long unsigned int]’: +hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ + 2915 | add_haplotypes(alts, + | ~~~~~~~~~~~~~~^~~~~~ + 2916 | haplotypes, + | ~~~~~~~~~~~ + 2917 | haplotype_maxrights, + | ~~~~~~~~~~~~~~~~~~~~ + 2918 | cmp_ht, + | ~~~~~~~ + 2919 | ht_list, + | ~~~~~~~~ + 2920 | rdlen); + | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ @@ -3603,106 +3737,82 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2801 | if(rfoff >= contig_len) return 0; - | ~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { - | ~~~~~^~~~~~~~ -hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 3161 | if(alignedLen == next_rdlen) return rdlen; - | ~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2879 | if(alt_range.first >= alts.size()) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] - 3044 | for(int i = 0; i < alt.len; i++) { - | ~~^~~~~~~~~ -hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 3454 | if(best_rdoff < rdoff + rd_i) { - | ~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] - 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { - | ~~~~~^~~~~~~~ -hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] - 3161 | if(alignedLen == next_rdlen) return rdlen; - | ~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] - 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] - 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] - 3454 | if(best_rdoff < rdoff + rd_i) { - | ~~~~~~~~~~~^~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ - 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ - 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ - 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ - 1453 | st_.back().init( - | ~~~~~~~~~~~~~~~^ - 1454 | gfmFw, // Bowtie index - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1455 | ref, // bitpair-encoded reference - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1456 | sa, // SA range with offsets - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1457 | st_, // EList - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1458 | hit_, // GWHit - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1459 | 0, // range 0 - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1460 | false, // put resolved elements into res_? - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1461 | NULL, // put resolved elements here - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1462 | top, // GBW row at top - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1463 | bot, // GBW row at bot - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1464 | node_top, // node at top - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1465 | node_bot, // node at bot - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1466 | sa.node_iedge_count, - | ~~~~~~~~~~~~~~~~~~~~ - 1467 | 0, // # steps taken - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1468 | met); // update metrics here - | ~~~~ -hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2660 | if(ht_range.first >= haplotypes.size()) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 2675 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 2713 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 2744 | if(ht_list[h].first == ht_range.second) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: +spliced_aligner.h:331:9: required from here + 331 | int64_t SplicedAligner::hybridSearch_recur( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] + 408 | bool another_spliced = false; + | ^~~~~~~~~~~~~~~ +spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] + 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] + 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from aligner_seed2.h:109, + from aligner_driver.h:78, + from hi_aligner.h:41: +group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ + 1517 | st.advance( + | ~~~~~~~~~~^ + 1518 | gfmFw, + | ~~~~~~ + 1519 | ref, + | ~~~~ + 1520 | sa, + | ~~~ + 1521 | hit_, + | ~~~~~ + 1522 | (index_t)range, + | ~~~~~~~~~~~~~~~ + 1523 | false, + | ~~~~~~ + 1524 | NULL, + | ~~~~~ + 1525 | st_, + | ~~~~ + 1526 | gws, + | ~~~~ + 1527 | met, + | ~~~~ + 1528 | prm); + | ~~~~ +hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ + 5901 | _gws_local.advanceElement( + | ~~~~~~~~~~~~~~~~~~~~~~~~~^ + 5902 | off, + | ~~~~ + 5903 | gfm, // forward Bowtie index for walking left + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5904 | ref, // bitpair-encoded reference + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5905 | _sas_local, // SA range with offsets + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5906 | _gwstate_local, // GroupWalk state; scratch space + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5907 | wr, // put the result here + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5908 | met, // metrics + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 5909 | prm); // per-read metrics + | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ @@ -3750,131 +3860,19 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 789 | if(new_top - top == tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 795 | if(i + 1 < tmp_zOffs.size()) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ - 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ - 1453 | st_.back().init( - | ~~~~~~~~~~~~~~~^ - 1454 | gfmFw, // Bowtie index - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1455 | ref, // bitpair-encoded reference - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1456 | sa, // SA range with offsets - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1457 | st_, // EList - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1458 | hit_, // GWHit - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1459 | 0, // range 0 - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1460 | false, // put resolved elements into res_? - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1461 | NULL, // put resolved elements here - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1462 | top, // GBW row at top - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1463 | bot, // GBW row at bot - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1464 | node_top, // node at top - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1465 | node_bot, // node at bot - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1466 | sa.node_iedge_count, - | ~~~~~~~~~~~~~~~~~~~~ - 1467 | 0, // # steps taken - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1468 | met); // update metrics here - | ~~~~ -hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ - 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ - 5664 | getGenomeCoords_local( - | ^~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ - 4107 | mate_found |= alignMate( - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 789 | if(new_top - top == tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 795 | if(i + 1 < tmp_zOffs.size()) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: -hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ - 2915 | add_haplotypes(alts, - | ~~~~~~~~~~~~~~^~~~~~ - 2916 | haplotypes, - | ~~~~~~~~~~~ - 2917 | haplotype_maxrights, - | ~~~~~~~~~~~~~~~~~~~~ - 2918 | cmp_ht, - | ~~~~~~~ - 2919 | ht_list, - | ~~~~~~~~ - 2920 | rdlen); - | ~~~~~~ +group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1147 | if(new_node_bot - new_node_top < gws.map.size()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { + | ~~~~~~^~~~~~~~~~~~~~~~ +group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ @@ -4044,23 +4042,219 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2660 | if(ht_range.first >= haplotypes.size()) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2675 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2713 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2744 | if(ht_list[h].first == ht_range.second) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long long unsigned int]’: -hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2801 | if(rfoff >= contig_len) return 0; + | ~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2879 | if(alt_range.first >= alts.size()) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 3044 | for(int i = 0; i < alt.len; i++) { + | ~~^~~~~~~~~ +hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { + | ~~~~~^~~~~~~~ +hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 3161 | if(alignedLen == next_rdlen) return rdlen; + | ~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long long unsigned int; TAlScore = long long int]’: +spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ + 494 | bool combined = tempHit.combineWith( + | ~~~~~~~~~~~~~~~~~~~^ + 495 | hit, + | ~~~~ + 496 | rd, + | ~~~ + 497 | gfm, + | ~~~~ + 498 | ref, + | ~~~~ + 499 | altdb, + | ~~~~~~ + 500 | repeatdb, + | ~~~~~~~~~ + 501 | ssdb, + | ~~~~~ + 502 | swa, + | ~~~~ + 503 | swm, + | ~~~~ + 504 | sc, + | ~~~ + 505 | minsc, + | ~~~~~~ + 506 | rnd, + | ~~~~ + 507 | (index_t)this->_minK_local, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 508 | (index_t)tpol.minIntronLen(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 509 | (index_t)tpol.maxIntronLen(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 510 | 1, + | ~~ + 511 | 1, + | ~~ + 512 | gpol.maxAltsTried(), + | ~~~~~~~~~~~~~~~~~~~~ + 513 | &ss, + | ~~~~ + 514 | tpol.no_spliced_alignment()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +spliced_aligner.h:331:9: required from here + 331 | int64_t SplicedAligner::hybridSearch_recur( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] + 1926 | if(alt.seq == rdc) { + | ~~~~~~~~^~~~~~ +hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 3454 | if(best_rdoff < rdoff + rd_i) { + | ~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ + 1086 | index_t nelt = this->globalGFMSearch( + | ~~~~~~~~~~~~~~~~~~~~~^ + 1087 | gfm, // GFM index + | ~~~~~~~~~~~~~~~~~~~~ + 1088 | rd, // read to align + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 1089 | sc, // scoring scheme + | ~~~~~~~~~~~~~~~~~~~~~~~~~ + 1090 | sink.reportingParams(), + | ~~~~~~~~~~~~~~~~~~~~~~~ + 1091 | hit.fw(), + | ~~~~~~~~~ + 1092 | extoff, + | ~~~~~~~ + 1093 | extlen, + | ~~~~~~~ + 1094 | top, + | ~~~~ + 1095 | bot, + | ~~~~ + 1096 | node_top, + | ~~~~~~~~~ + 1097 | node_bot, + | ~~~~~~~~~ + 1098 | this->_node_iedge_count, + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 1099 | rnd, + | ~~~~ + 1100 | uniqueStop); + | ~~~~~~~~~~~ +spliced_aligner.h:331:9: required from here + 331 | int64_t SplicedAligner::hybridSearch_recur( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ + 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ + 1453 | st_.back().init( + | ~~~~~~~~~~~~~~~^ + 1454 | gfmFw, // Bowtie index + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1455 | ref, // bitpair-encoded reference + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1456 | sa, // SA range with offsets + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1457 | st_, // EList + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1458 | hit_, // GWHit + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1459 | 0, // range 0 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1460 | false, // put resolved elements into res_? + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1461 | NULL, // put resolved elements here + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1462 | top, // GBW row at top + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1463 | bot, // GBW row at bot + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1464 | node_top, // node at top + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1465 | node_bot, // node at bot + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1466 | sa.node_iedge_count, + | ~~~~~~~~~~~~~~~~~~~~ + 1467 | 0, // # steps taken + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1468 | met); // update metrics here + | ~~~~ +hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ + 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ + 5664 | getGenomeCoords_local( + | ^~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ + 4107 | mate_found |= alignMate( + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 789 | if(new_top - top == tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 795 | if(i + 1 < tmp_zOffs.size()) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: +hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, @@ -4073,7 +4267,7 @@ | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, @@ -4132,7 +4326,7 @@ | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, @@ -4175,7 +4369,7 @@ | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, @@ -4198,7 +4392,7 @@ | ~~~~ 5702 | gpol); | ~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here @@ -4245,75 +4439,18 @@ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ - 1071 | OFF_MASK, begin, end); - | ^~~~~~~~ -multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ - 914 | off = OFF_MASK; - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ - 923 | OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ - 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( @@ -4321,19 +4458,6 @@ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ -spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: -spliced_aligner.h:331:9: required from here - 331 | int64_t SplicedAligner::hybridSearch_recur( - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] - 408 | bool another_spliced = false; - | ^~~~~~~~~~~~~~~ -spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] - 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] - 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long long int]’: spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ 494 | bool combined = tempHit.combineWith( @@ -4384,94 +4508,6 @@ hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] 1926 | if(alt.seq == rdc) { | ~~~~~~~~^~~~~~ -hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long long unsigned int; TAlScore = long long int]’: -spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ - 494 | bool combined = tempHit.combineWith( - | ~~~~~~~~~~~~~~~~~~~^ - 495 | hit, - | ~~~~ - 496 | rd, - | ~~~ - 497 | gfm, - | ~~~~ - 498 | ref, - | ~~~~ - 499 | altdb, - | ~~~~~~ - 500 | repeatdb, - | ~~~~~~~~~ - 501 | ssdb, - | ~~~~~ - 502 | swa, - | ~~~~ - 503 | swm, - | ~~~~ - 504 | sc, - | ~~~ - 505 | minsc, - | ~~~~~~ - 506 | rnd, - | ~~~~ - 507 | (index_t)this->_minK_local, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 508 | (index_t)tpol.minIntronLen(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 509 | (index_t)tpol.maxIntronLen(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 510 | 1, - | ~~ - 511 | 1, - | ~~ - 512 | gpol.maxAltsTried(), - | ~~~~~~~~~~~~~~~~~~~~ - 513 | &ss, - | ~~~~ - 514 | tpol.no_spliced_alignment()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -spliced_aligner.h:331:9: required from here - 331 | int64_t SplicedAligner::hybridSearch_recur( - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] - 1926 | if(alt.seq == rdc) { - | ~~~~~~~~^~~~~~ -hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ - 1086 | index_t nelt = this->globalGFMSearch( - | ~~~~~~~~~~~~~~~~~~~~~^ - 1087 | gfm, // GFM index - | ~~~~~~~~~~~~~~~~~~~~ - 1088 | rd, // read to align - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 1089 | sc, // scoring scheme - | ~~~~~~~~~~~~~~~~~~~~~~~~~ - 1090 | sink.reportingParams(), - | ~~~~~~~~~~~~~~~~~~~~~~~ - 1091 | hit.fw(), - | ~~~~~~~~~ - 1092 | extoff, - | ~~~~~~~ - 1093 | extlen, - | ~~~~~~~ - 1094 | top, - | ~~~~ - 1095 | bot, - | ~~~~ - 1096 | node_top, - | ~~~~~~~~~ - 1097 | node_bot, - | ~~~~~~~~~ - 1098 | this->_node_iedge_count, - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 1099 | rnd, - | ~~~~ - 1100 | uniqueStop); - | ~~~~~~~~~~~ -spliced_aligner.h:331:9: required from here - 331 | int64_t SplicedAligner::hybridSearch_recur( - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -4889,15 +4925,6 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from edit.h:26, - from edit.cpp:21: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -4918,8 +4945,15 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30: +In file included from edit.h:26, + from edit.cpp:21: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -4935,6 +4969,8 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5057,16 +5093,6 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from alphabet.h:27, - from gfm.h:40, - from gfm.cpp:21: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -5077,6 +5103,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from alphabet.h:27, + from gfm.h:40: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ +In file included from alphabet.h:27, + from gfm.h:40, + from gfm.cpp:21: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5092,15 +5137,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from alphabet.h:27, - from gfm.h:40: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5361,31 +5397,6 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.h:59: -In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, - inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, - inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, - inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, - inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: -repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized [-Wmaybe-uninitialized] - 41 | if(fw != o.fw) - | ~~^~ -repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -repeat.h:464:30: note: ‘cmp’ declared here - 464 | RepeatCoord cmp; - | ^~~ -In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, - inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, - inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, - inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, - inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: -repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized [-Wmaybe-uninitialized] - 43 | if(alleleID != o.alleleID) - | ~~^~~~~~~~ -repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -repeat.h:464:30: note: ‘cmp’ declared here - 464 | RepeatCoord cmp; - | ^~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -5536,32 +5547,31 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from sequence_io.h:30, - from hisat2_build.cpp:28: -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ +In file included from gfm.h:59: +In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, + inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, + inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, + inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, + inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: +repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized [-Wmaybe-uninitialized] + 41 | if(fw != o.fw) + | ~~^~ +repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +repeat.h:464:30: note: ‘cmp’ declared here + 464 | RepeatCoord cmp; + | ^~~ +In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, + inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, + inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, + inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, + inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: +repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized [-Wmaybe-uninitialized] + 43 | if(alleleID != o.alleleID) + | ~~^~~~~~~~ +repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +repeat.h:464:30: note: ‘cmp’ declared here + 464 | RepeatCoord cmp; + | ^~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -5712,28 +5722,29 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from sequence_io.h:30: +In file included from sequence_io.h:30, + from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:768:29: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:766:29: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ @@ -5761,27 +5772,28 @@ sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ +In file included from sequence_io.h:30: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ @@ -5935,6 +5947,45 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: @@ -5953,21 +6004,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -6119,6 +6155,13 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -6131,13 +6174,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -9873,8 +9909,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_i386.deb'. -dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-5_i386.deb'. +dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_i386.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9882,12 +9918,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/11177/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11177/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/92221 and its subdirectories -I: Current time: Mon Mar 9 15:03:02 -12 2026 -I: pbuilder-time-stamp: 1773111782 +I: removing directory /srv/workspace/pbuilder/11177 and its subdirectories +I: Current time: Wed Feb 5 10:45:32 +14 2025 +I: pbuilder-time-stamp: 1738701932