sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | hisat2 2.2.1-5 (amd64) Thu, 09 Jul 2026 13:12:07 +0000 | +==============================================================================+ Package: hisat2 Version: 2.2.1-5 Source Version: 2.2.1-5 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Thu, 09 Jul 2026 13:12:09 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hisat2_2.2.1-5 perl-5.44-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hisat2_2.2.1-5 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 09 Jul 2026 13:12:09 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:3 http://deb.debian.org/debian sid InRelease [193 kB] Err:3 http://deb.debian.org/debian sid InRelease Sub-process /usr/bin/sqv returned an error code (1), error message is: Verifying signature: Message has been manipulated Verifying signature: Message has been manipulated Fetched 193 kB in 4s (44.4 kB/s) Reading package lists... W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. OpenPGP signature verification failed: http://deb.debian.org/debian sid InRelease: Sub-process /usr/bin/sqv returned an error code (1), error message is: Verifying signature: Message has been manipulated Verifying signature: Message has been manipulated W: Failed to fetch http://deb.debian.org/debian/dists/sid/InRelease Sub-process /usr/bin/sqv returned an error code (1), error message is: Verifying signature: Message has been manipulated Verifying signature: Message has been manipulated W: Some index files failed to download. They have been ignored, or old ones used instead. Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Thu, 09 Jul 2026 13:12:16 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/hisat2_2.2.1-5.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 09 Jul 2026 13:12:17 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, build-essential Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive ./ InRelease Get:2 copy:/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive ./ Release [609 B] Ign:3 copy:/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive ./ Release.gpg Get:4 copy:/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive ./ Sources [672 B] Get:5 copy:/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive ./ Packages [684 B] Fetched 1965 B in 0s (149 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libexpat1 libfile-stripnondeterminism-perl liblocale-gettext-perl liblua5.4-0 libmagic-mgc libmagic1t64 libnuma1 libpipeline1 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libsimde-dev libtool libuchardet0 libxml2-16 libyaml-0-2 m4 man-db media-types netbase pandoc pandoc-data po-debconf python3 python3-minimal python3.14 python3.14-minimal sensible-utils tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser citation-style-language-styles context ghc libjs-katex libjs-mathjax librsvg2-bin nodejs pandoc-citeproc php r-base-core ruby texlive-latex-extra texlive-latex-recommended texlive-luatex texlive-xetex wkhtmltopdf libmail-box-perl python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libexpat1 libfile-stripnondeterminism-perl liblocale-gettext-perl liblua5.4-0 libmagic-mgc libmagic1t64 libnuma1 libpipeline1 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libsimde-dev libtool libuchardet0 libxml2-16 libyaml-0-2 m4 man-db media-types netbase pandoc pandoc-data po-debconf python3 python3-minimal python3.14 python3.14-minimal sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 49.1 MB/49.1 MB of archives. After this operation, 306 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 liblocale-gettext-perl amd64 1.07-10+b1 [15.1 kB] Get:2 copy:/build/hisat2-jwYPXf/resolver-pVOpwz/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [884 B] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.6-1 [896 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.6-1 [2416 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.6-1 [25.1 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.6-1 [2278 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.6-1 [846 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.6-1 [8108 B] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.6-1 [25.1 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:35 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.8-2 [148 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.4~rc3-5 [500 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2+b1 [53.8 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.10-1 [531 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.10-1 [28.8 MB] Preconfiguring packages ... Fetched 49.1 MB in 0s (152 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 14518 files and directories currently installed.) Preparing to unpack .../libexpat1_2.8.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.2-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-10+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-10+b1) ... Selecting previously unselected package libpython3.14-minimal:amd64. Preparing to unpack .../libpython3.14-minimal_3.14.6-1_amd64.deb ... Unpacking libpython3.14-minimal:amd64 (3.14.6-1) ... Selecting previously unselected package python3.14-minimal. Preparing to unpack .../python3.14-minimal_3.14.6-1_amd64.deb ... Unpacking python3.14-minimal (3.14.6-1) ... Setting up libpython3.14-minimal:amd64 (3.14.6-1) ... Setting up libexpat1:amd64 (2.8.2-1) ... Setting up python3.14-minimal (3.14.6-1) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../36-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up libsimde-dev (0.8.4~rc3-5) ... Setting up bsdextrautils (2.42.2-1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2+b1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libdebhelper-perl (14.3) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up gettext-base (1.0-3) ... Setting up m4 (1.4.21-1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up tzdata (2026b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jul 9 13:12:28 UTC 2026. Universal Time is now: Thu Jul 9 13:12:28 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1+nmu1) ... Setting up autopoint (1.0-3) ... Setting up autoconf (2.73-2) ... Setting up libnuma1:amd64 (2.0.19-1+b2) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up liblua5.4-0:amd64 (5.4.8-2) ... Setting up netbase (6.5) ... Setting up pandoc-data (3.10-1) ... Setting up liblocale-gettext-perl (1.07-10+b1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libtool (2.5.4-11) ... Setting up libpython3.14-stdlib:amd64 (3.14.6-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (22) ... Setting up pandoc (3.10-1) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up python3.14 (3.14.6-1) ... Setting up libpython3-stdlib:amd64 (3.14.6-1) ... Setting up po-debconf (1.0.22) ... Setting up python3 (3.14.6-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (14.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 09 Jul 2026 13:12:30 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Thu, 09 Jul 2026 13:12:31 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 help2man_1.49.3 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libexpat1_2.8.2-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libhogweed6t64_3.10.2-1+b1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libksba8_1.8.0-3 libldap2_2.6.13+dfsg-1+b1 liblocale-gettext-perl_1.07-10+b1 liblsan0_16.1.0-2 liblua5.4-0_5.4.8-2 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnpth0t64_1.8-3+b2 libnuma1_2.0.19-1+b2 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libpython3-stdlib_3.14.6-1 libpython3.14-minimal_3.14.6-1 libpython3.14-stdlib_3.14.6-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libyaml-0-2_0.2.5-2+b1 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 netbase_6.5 openssl-provider-legacy_3.6.3-1 pandoc_3.10-1 pandoc-data_3.10-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.2-4 po-debconf_1.0.22 python3_3.14.6-1 python3-minimal_3.14.6-1 python3.14_3.14.6-1 python3.14-minimal_3.14.6-1 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tzdata_2026b-1 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Thu, 09 Jul 2026 13:12:31 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hisat2 Binary: hisat2, python3-hisat2 Architecture: any all Version: 2.2.1-5 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://daehwankimlab.github.io/hisat2/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/hisat2 Vcs-Git: https://salsa.debian.org/med-team/hisat2.git Testsuite: autopkgtest Testsuite-Triggers: bcftools, samtools Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man , pandoc , python3:any Package-List: hisat2 deb science optional arch=any python3-hisat2 deb python optional arch=all Checksums-Sha1: e09c36d93952eff1ebfd19545c38e173636bf662 6761242 hisat2_2.2.1.orig.tar.gz 96871cfbd92f3e6d11393aba14344550f57ff8d2 29576 hisat2_2.2.1-5.debian.tar.xz Checksums-Sha256: f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 6761242 hisat2_2.2.1.orig.tar.gz 70d19cce728774d945e65a341721be568980cbd42c4449e8cb4677850c62607d 29576 hisat2_2.2.1-5.debian.tar.xz Files: 0d1fcfcaf7ba1e64eb68006bba5a3855 6761242 hisat2_2.2.1.orig.tar.gz 0168dcca6cecdd97887bb4330c189aaa 29576 hisat2_2.2.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmaNEIYACgkQPCZ2P2xn 5uKpuw/9HA+ly3oYGrYHwPjr4hsKtUAqP6YK1GgbrVylLefTL1kjIwr7m6hNGCzu 99X3wix8CRksJoEqqxw3TyVlMx9f4NQ247lKsJrejwGBK7S+GB5h2SgnKIYqUkKM Wgl/BkMQWgAYR1zHJ/nx+DD/gjx3ZqlG9JHzaECFTrIMdhHprWnOX5wGLZhaRpZA uKBFQqvYUVOIc5gyBZqP+tynQAqPk9cQ4YfcAU037Ew7ANtyxq+8DeXfgpn/t7lA /uba4uCfs7rxm4PmH/rroSrrny7nkF5YZiWd0wMIHkiWvty0fdgVJ1Y3rg/IgAgi 2fLJSRT7jVx2V8LfOcolXOMIC6pCsltpKG8WY42lZTB1nIUpR46i0OG+fVUAhd5N 4FsmK3YnBUBfY6Nx/CWq6SL1MzxdKoDxC88i4P8Ie6tZZxTJi5G0o8WCX/UgB4uS llD1hPGJVGszV4eTQyjNBk798Ac0+x2joThxuiwHedyG/41AyYXAUGJ7XJnITqPm GNeBvCZAJxtDyz9bmAPEAIteP9FczwWZHEB16IYB8pG+pwfRd7Dp/BFYQWwyVaD2 m6FEF/spuP9m5IdbwHbx2uEKxWGtm/bYBqSKdIGoyPFMMRu9aAlG70iaWKC2n+QL Aqq/FvUD9DBcfDfU5IqL07a2QYgECbcgR0gANrC9Yamz4Jzu7rc= =vP68 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-5.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./hisat2_2.2.1-5.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting hisat2 in /build/hisat2-jwYPXf/hisat2-2.2.1 dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_imp dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 dpkg-source: info: applying fix-manual dpkg-source: info: applying riscv5 clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Thu, 09 Jul 2026 13:12:32 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hisat2_2.2.1-5 perl-5.44-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hisat2_2.2.1-5 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/hisat2-jwYPXf/hisat2-2.2.1 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-73d5581d-0749-4812-a6c5-015df11b8c3c SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/build/hisat2-jwYPXf/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 \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so make[1]: Leaving directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building hisat2 using existing ../hisat2_2.2.1.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building hisat2 in ../hisat2_2.2.1-5.debian.tar.xz dpkg-source: info: building hisat2 in ../hisat2_2.2.1-5.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="09 July 2024" all doc make -j2 INSTALL="install --strip-program=true" BUILD_HOST=Debian BUILD_TIME="09 July 2024" all doc make[2]: Entering directory '/build/hisat2-jwYPXf/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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now 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] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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 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] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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 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 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 unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = 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: 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( | ~~~~~~~~~~~~~~~~~~~~^ 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 = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = 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 gfm.h:63: In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:960:49, inlined from ‘LocalGFM::LocalGFM(TStr&, const EList&, PathGraph*, full_index_t, full_index_t, full_index_t, EList >&, index_t, bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, std::ostream&, std::ostream&, int32_t, bool, bool, bool) [with TStr = SString; index_t = short unsigned int; full_index_t = long unsigned int]’ at hgfm.h:182:29: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In function ‘LocalGFM::LocalGFM(TStr&, const EList&, PathGraph*, full_index_t, full_index_t, full_index_t, EList >&, index_t, bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, std::ostream&, std::ostream&, int32_t, bool, bool, bool) [with TStr = SString; index_t = short unsigned int; full_index_t = long unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In file included from gfm.h:63: In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:960:49, inlined from ‘LocalGFM::LocalGFM(TStr&, const EList&, PathGraph*, full_index_t, full_index_t, full_index_t, EList >&, index_t, bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, std::ostream&, std::ostream&, int32_t, bool, bool, bool) [with TStr = SString; index_t = short unsigned int; full_index_t = unsigned int]’ at hgfm.h:182:29: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In function ‘LocalGFM::LocalGFM(TStr&, const EList&, PathGraph*, full_index_t, full_index_t, full_index_t, EList >&, index_t, bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, std::ostream&, std::ostream&, int32_t, bool, bool, bool) [with TStr = SString; index_t = short unsigned int; full_index_t = unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined 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]’ at gfm.h:1017:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘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]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with index_t = unsigned int]’ at gfm.h:960:49, inlined from ‘LocalRFM::LocalRFM(TStr&, InorderBlockwiseSA*, PathGraph*, EList >&, index_t, const EList >&, bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, std::ostream&, std::ostream&, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:161:29, 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:843:9: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘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]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ 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 member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined 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 unsigned int]’ at gfm.h:1017:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘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 unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with index_t = long unsigned int]’ at gfm.h:960:49, inlined from ‘LocalRFM::LocalRFM(TStr&, InorderBlockwiseSA*, PathGraph*, EList >&, index_t, const EList >&, bool, int, int32_t, int32_t, int32_t, const std::string&, bool, int, EList&, index_t, const RefReadInParams&, uint32_t, std::ostream&, std::ostream&, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:161:29, 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 = long unsigned int]’ at rfm.h:843:9: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘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 unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ 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 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 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 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 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 ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ 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 = 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 = 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 = 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 = 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 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 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 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 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]; | ^~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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; | ^~~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~ /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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ 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 ‘< >’ 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ 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 unsigned int; local_index_t = short unsigned int]’: 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); | ~~~~~~~~~~ hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] 4404 | if(positions[p].first.tid != res.refid()) continue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 4405 | if(positions[p].first.toff + 1000 < res.refoff() || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); | ~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h: In instantiation of ‘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: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); | ~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4088:17: 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 unsigned int; local_index_t = short unsigned int]’ 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ 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); | ~~~~~~~~~~ hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5990 | if(_repeatConcordant[r].first == left.off() && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5991 | _repeatConcordant[r].second == left2.off()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 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; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘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 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 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); | ~~~~~~~~~~ hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { | ~~~~~^~~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long 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; | ^~~~~~~~ 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 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 unsigned int; local_index_t = short unsigned int]’ 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: 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 unsigned int; local_index_t = short unsigned int]’ 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ 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); | ~~~~~~~~~~ hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 5150 | if(coord.ref() == numeric_limits::max()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘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 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 unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 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 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); | ~~~~~~~~~~ hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 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]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 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]’ 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); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 = long 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 = 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 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 ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 = 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 unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 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 unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 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 unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 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 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); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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 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 ‘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 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 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 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 unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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); | ~~~~~~ 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, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 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]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 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]’ 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); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.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 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 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 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 ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 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 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 unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 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 unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 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 unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 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 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); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 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 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 ‘long 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 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 = unsigned int; local_index_t = short unsigned int; int64_t = 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: 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 unsigned int; local_index_t = short unsigned int; int64_t = 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 unsigned int’ and ‘int64_t’ {aka ‘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 unsigned int’ and ‘int64_t’ {aka ‘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 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 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 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 unsigned int; TAlScore = 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 unsigned int; local_index_t = short unsigned int; int64_t = 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 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 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 unsigned int; local_index_t = short unsigned int; int64_t = 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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:63: In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In file included from gfm.h:63: In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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 splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included 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_sw.cpp:25: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_sw.cpp:25: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included 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: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_ee_i16.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_ee_i16.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_u8.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_u8.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_ee_u8.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_ee_u8.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ /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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now 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] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ 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)’: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ 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)’: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.h:63: In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In file included from gfm.h:63: In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ In member function ‘bool ProcessorSupport::POPCNTenabled()’, inlined from ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’ at gfm.h:682:49: processor_support.h:57:26: warning: ‘regs.regs_t::ECX’ may be used uninitialized [-Wmaybe-uninitialized] 57 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ~~~~~~~~~~^~~~~~~~~~ processor_support.h: In constructor ‘GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short unsigned int]’: processor_support.h:43:12: note: ‘regs.regs_t::ECX’ was declared here 43 | regs_t regs; | ^~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ 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 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()); | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ 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 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()); | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ 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()); | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ 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()); | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /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/hisat2-jwYPXf/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from hisat2_repeat.cpp:36: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from hisat2_repeat.cpp:37: 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 ‘< >’ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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 splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included 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_sw.cpp:25: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_ee_i16.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_ee_u8.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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_u8.cpp:56: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included 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 bit_packed_array.cpp:24: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 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 repeat_builder.cpp:26: 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++/15/memory:80, from gfm.h:28: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | 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++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: 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 ‘< >’ repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~ repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^ repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 403 | for(size_t i = 0; i < num_cached_; i++) { | ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^ repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~ repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { | ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1277 | if(i == seq_len - 1) ed2[i] = add; | ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^ repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^ repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2926 | for(size_t i = 0; i < head_len; i++) { | ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^ repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31: repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] 947 | CoordHelper coordHelper_; | ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] 940 | bool forward_only_; | ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] 3167 | RepeatBuilder::RepeatBuilder(TStr& s, | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3396 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3426 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3553 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3563 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 4114 | if((oskip + out_len) == output_width) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: repeat_builder.cpp:4754:46: required from here 4754 | template void dump_tstr(const SString& ); | ^ repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { | ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ~~~~~~~^ repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; size_t = long unsigned int]’: repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3312 | query = getString(s_, i, rp.min_repeat_len); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long unsigned int; size_t = long unsigned int; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ In file included from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from repeat_builder.cpp:21: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: /usr/include/c++/15/bits/ostream.h:179:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] 179 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here 3664 | TIndexOffU pos_in_chr; | ^~~~~~~~~~ make[2]: Leaving directory '/build/hisat2-jwYPXf/hisat2-2.2.1' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \ --no-info > debian/hisat2-align-l.1 help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \ --no-info > debian/hisat2-align-s.1 help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \ --no-info > debian/hisat2-build.1 #rm hisat2-buildc help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \ --no-info > debian/hisat2-build-l.1 help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \ --no-info > debian/hisat2-build-s.1 help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \ --no-info > debian/hisat2-inspect.1 help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 make[1]: Leaving directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.4~rc3-5), " make[1]: Leaving directory '/build/hisat2-jwYPXf/hisat2-2.2.1' dh_md5sums dh_builddeb 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_amd64.deb'. dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_amd64.deb'. dpkg-genbuildinfo -O../hisat2_2.2.1-5_amd64.buildinfo dpkg-genchanges -O../hisat2_2.2.1-5_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-07-09T13:19:05Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 09 Jul 2026 13:19:05 +0000 | +------------------------------------------------------------------------------+ hisat2_2.2.1-5_amd64.changes: ----------------------------- Format: 1.8 Date: Tue, 09 Jul 2024 12:26:53 +0200 Source: hisat2 Binary: hisat2 hisat2-dbgsym python3-hisat2 Architecture: source amd64 all Version: 2.2.1-5 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: hisat2 - graph-based alignment of short nucleotide reads to many genomes python3-hisat2 - Python scripts accompanying hisat2 Closes: 1074739 Changes: hisat2 (2.2.1-5) unstable; urgency=medium . * d/patches/no_imp: add Python3.12 support. 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459ca1d7e9b29119afbaf5e95e5b1aba8a17bd67a5bf18d05f88adcd3b353479 13284 python3-hisat2_2.2.1-5_all.deb Files: 1100df15d34d5e546104ecbd4e71f526 1221 science optional hisat2_2.2.1-5.dsc 0168dcca6cecdd97887bb4330c189aaa 29576 science optional hisat2_2.2.1-5.debian.tar.xz a161dd426396ee04af7ff01bd2c4b5de 13710164 debug optional hisat2-dbgsym_2.2.1-5_amd64.deb 0ec45140d936b4f9f22d68983c90d3dc 6098 science optional hisat2_2.2.1-5_amd64.buildinfo 3795d4bb475917d002c555a5b895f0e8 3835856 science optional hisat2_2.2.1-5_amd64.deb 814810b7648ec1fb3363da03dc990f8d 13284 python optional python3-hisat2_2.2.1-5_all.deb +------------------------------------------------------------------------------+ | Buildinfo Thu, 09 Jul 2026 13:19:05 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: hisat2 Binary: hisat2 hisat2-dbgsym python3-hisat2 Architecture: all amd64 source Version: 2.2.1-5 Checksums-Md5: 1100df15d34d5e546104ecbd4e71f526 1221 hisat2_2.2.1-5.dsc a161dd426396ee04af7ff01bd2c4b5de 13710164 hisat2-dbgsym_2.2.1-5_amd64.deb 3795d4bb475917d002c555a5b895f0e8 3835856 hisat2_2.2.1-5_amd64.deb 814810b7648ec1fb3363da03dc990f8d 13284 python3-hisat2_2.2.1-5_all.deb Checksums-Sha1: 7ecb309cdc32ede8e09939ae2fae8e17e3db54ca 1221 hisat2_2.2.1-5.dsc 2ec1f87d197e44f1ee2b00763ad6ccbdabd641f4 13710164 hisat2-dbgsym_2.2.1-5_amd64.deb d798a9d8006f60d7d9d4323b1e7cb8edefb42269 3835856 hisat2_2.2.1-5_amd64.deb e464eedf39499fa45316a7b30eafa56370be083d 13284 python3-hisat2_2.2.1-5_all.deb Checksums-Sha256: 0023dc1cb03f0b28c0846b2272a1222acb6864d14d5c16a1b4c0ee3fc1548414 1221 hisat2_2.2.1-5.dsc 456e293b6785b2e151519acce1146312d219b56d5df2d300e40ef51db92e37ae 13710164 hisat2-dbgsym_2.2.1-5_amd64.deb d2cf73693d2b9c0356ca5b00720b25eb6a9363c8a033549a1f99b4c8bdae0d01 3835856 hisat2_2.2.1-5_amd64.deb 459ca1d7e9b29119afbaf5e95e5b1aba8a17bd67a5bf18d05f88adcd3b353479 13284 python3-hisat2_2.2.1-5_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 09 Jul 2026 13:19:04 +0000 Build-Path: /build/hisat2-jwYPXf/hisat2-2.2.1 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libexpat1 (= 2.8.2-1), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libhwasan0 (= 16.1.0-2), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), liblocale-gettext-perl (= 1.07-10+b1), liblsan0 (= 16.1.0-2), liblua5.4-0 (= 5.4.8-2), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncursesw6 (= 6.6+20260608-2), libnuma1 (= 2.0.19-1+b2), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libpython3-stdlib (= 3.14.6-1), libpython3.14-minimal (= 3.14.6-1), libpython3.14-stdlib (= 3.14.6-1), libquadmath0 (= 16.1.0-2), libreadline8t64 (= 8.3-4), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42.2-1), libsqlite3-0 (= 3.53.3-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libyaml-0-2 (= 0.2.5-2+b1), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), netbase (= 6.5), openssl-provider-legacy (= 3.6.3-1), pandoc (= 3.10-1), pandoc-data (= 3.10-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), po-debconf (= 1.0.22), python3 (= 3.14.6-1), python3-minimal (= 3.14.6-1), python3.14 (= 3.14.6-1), python3.14-minimal (= 3.14.6-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tzdata (= 2026b-1), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1720520813" +------------------------------------------------------------------------------+ | Package contents Thu, 09 Jul 2026 13:19:05 +0000 | +------------------------------------------------------------------------------+ hisat2-dbgsym_2.2.1-5_amd64.deb ------------------------------- new Debian package, version 2.0. size 13710164 bytes: control archive=848 bytes. 573 bytes, 12 lines control 719 bytes, 7 lines md5sums Package: hisat2-dbgsym Source: hisat2 Version: 2.2.1-5 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 14239 Depends: hisat2 (= 2.2.1-5) Section: debug Priority: optional Description: debug symbols for hisat2 Build-Ids: 189f2942b810a7c4e8e39826571cb47821e33749 322fbd47e3b85b0794bed1dca44953fb68fc2aec 76fc1e19c22efb59eabbc30f992892b510997406 8050bd46cf7ea32b41849cc9e06b30de4edd5d56 9180d2fbcdde594f93f560af2a5638bd79ad69f1 b2a56bb467feb4530e55fff920a2609bc5347bcb drwxr-xr-x root/root 0 2024-07-09 10:26 ./ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/18/ -rw-r--r-- root/root 2095024 2024-07-09 10:26 ./usr/lib/debug/.build-id/18/9f2942b810a7c4e8e39826571cb47821e33749.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/32/ -rw-r--r-- root/root 2093176 2024-07-09 10:26 ./usr/lib/debug/.build-id/32/2fbd47e3b85b0794bed1dca44953fb68fc2aec.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/76/ -rw-r--r-- root/root 3619456 2024-07-09 10:26 ./usr/lib/debug/.build-id/76/fc1e19c22efb59eabbc30f992892b510997406.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/80/ -rw-r--r-- root/root 3616960 2024-07-09 10:26 ./usr/lib/debug/.build-id/80/50bd46cf7ea32b41849cc9e06b30de4edd5d56.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/91/ -rw-r--r-- root/root 1186888 2024-07-09 10:26 ./usr/lib/debug/.build-id/91/80d2fbcdde594f93f560af2a5638bd79ad69f1.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.build-id/b2/ -rw-r--r-- root/root 1177136 2024-07-09 10:26 ./usr/lib/debug/.build-id/b2/a56bb467feb4530e55fff920a2609bc5347bcb.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 770904 2024-07-09 10:26 ./usr/lib/debug/.dwz/x86_64-linux-gnu/hisat2.debug drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-07-09 10:26 ./usr/share/doc/hisat2-dbgsym -> hisat2 hisat2_2.2.1-5_amd64.deb ------------------------ new Debian package, version 2.0. size 3835856 bytes: control archive=1844 bytes. 1293 bytes, 23 lines control 2420 bytes, 33 lines md5sums Package: hisat2 Version: 2.2.1-5 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 14837 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Built-Using: simde (= 0.8.4~rc3-5) Section: science Priority: optional Homepage: https://daehwankimlab.github.io/hisat2/ Description: graph-based alignment of short nucleotide reads to many genomes HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). drwxr-xr-x root/root 0 2024-07-09 10:26 ./ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/bin/ -rwxr-xr-x root/root 19908 2024-07-09 10:26 ./usr/bin/hisat2 -rwxr-xr-x root/root 2030856 2024-07-09 10:26 ./usr/bin/hisat2-align-l -rwxr-xr-x root/root 2010376 2024-07-09 10:26 ./usr/bin/hisat2-align-s -rwxr-xr-x root/root 2804 2024-07-09 10:26 ./usr/bin/hisat2-build -rwxr-xr-x root/root 1101024 2024-07-09 10:26 ./usr/bin/hisat2-build-l -rwxr-xr-x root/root 1076448 2024-07-09 10:26 ./usr/bin/hisat2-build-s -rwxr-xr-x root/root 3176 2024-07-09 10:26 ./usr/bin/hisat2-inspect -rwxr-xr-x root/root 597888 2024-07-09 10:26 ./usr/bin/hisat2-inspect-l -rwxr-xr-x root/root 606080 2024-07-09 10:26 ./usr/bin/hisat2-inspect-s drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/doc/hisat2/ -rw-r--r-- root/root 20092 2020-07-24 20:07 ./usr/share/doc/hisat2/MANUAL.gz -rw-r--r-- root/root 480 2024-07-09 10:26 ./usr/share/doc/hisat2/changelog.Debian.gz -rw-r--r-- root/root 2321 2024-07-09 10:06 ./usr/share/doc/hisat2/copyright drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/doc/hisat2/examples/ drwxr-xr-x root/root 0 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/ -rw-r--r-- root/root 4789374 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.1.ht2 -rw-r--r-- root/root 238700 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.2.ht2 -rw-r--r-- root/root 26 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.3.ht2 -rw-r--r-- root/root 225000 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.4.ht2 -rw-r--r-- root/root 678405 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.5.ht2 -rw-r--r-- root/root 238590 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.6.ht2 -rw-r--r-- root/root 70048 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.7.ht2 -rw-r--r-- root/root 37688 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.8.ht2 drwxr-xr-x root/root 0 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/reads/ -rw-r--r-- root/root 105893 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/reads/reads_1.fa -rw-r--r-- root/root 105893 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/reads/reads_2.fa drwxr-xr-x root/root 0 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/reference/ -rw-r--r-- root/root 1016689 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/reference/22_20-21M.fa -rw-r--r-- root/root 167831 2020-07-24 20:07 ./usr/share/doc/hisat2/examples/reference/22_20-21M.snp drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/man/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/man/man1/ -rw-r--r-- root/root 3642 2024-07-09 10:26 ./usr/share/man/man1/hisat2-align-l.1.gz -rw-r--r-- root/root 3641 2024-07-09 10:26 ./usr/share/man/man1/hisat2-align-s.1.gz -rw-r--r-- root/root 1167 2024-07-09 10:26 ./usr/share/man/man1/hisat2-build-l.1.gz -rw-r--r-- root/root 1164 2024-07-09 10:26 ./usr/share/man/man1/hisat2-build-s.1.gz -rw-r--r-- root/root 1219 2024-07-09 10:26 ./usr/share/man/man1/hisat2-build.1.gz -rw-r--r-- root/root 931 2024-07-09 10:26 ./usr/share/man/man1/hisat2-inspect-l.1.gz -rw-r--r-- root/root 929 2024-07-09 10:26 ./usr/share/man/man1/hisat2-inspect-s.1.gz -rw-r--r-- root/root 976 2024-07-09 10:26 ./usr/share/man/man1/hisat2-inspect.1.gz -rw-r--r-- root/root 3841 2024-07-09 10:26 ./usr/share/man/man1/hisat2.1.gz python3-hisat2_2.2.1-5_all.deb ------------------------------ new Debian package, version 2.0. size 13284 bytes: control archive=1264 bytes. 1315 bytes, 27 lines control 533 bytes, 7 lines md5sums Package: python3-hisat2 Source: hisat2 Version: 2.2.1-5 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 79 Depends: hisat2, python3 Built-Using: simde (= 0.8.4~rc3-5) Section: python Priority: optional Homepage: https://daehwankimlab.github.io/hisat2/ Description: Python scripts accompanying hisat2 HISAT2 is a fast and sensitive alignment program for mapping next- generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). . This package provides a serires of platform-independent scripts that are typically expected to be co-installed with the hisat2 binary. drwxr-xr-x root/root 0 2024-07-09 10:26 ./ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/bin/ -rwxr-xr-x root/root 5571 2024-07-09 10:26 ./usr/bin/hisat2_extract_exons.py -rwxr-xr-x root/root 19405 2024-07-09 10:26 ./usr/bin/hisat2_extract_snps_haplotypes_UCSC.py -rwxr-xr-x root/root 35214 2024-07-09 10:26 ./usr/bin/hisat2_extract_snps_haplotypes_VCF.py -rwxr-xr-x root/root 5043 2024-07-09 10:26 ./usr/bin/hisat2_extract_splice_sites.py drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/doc/python3-hisat2/ -rw-r--r-- root/root 485 2024-07-09 10:26 ./usr/share/doc/python3-hisat2/changelog.Debian.gz -rw-r--r-- root/root 2321 2024-07-09 10:06 ./usr/share/doc/python3-hisat2/copyright drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-07-09 10:26 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 123 2024-07-09 10:06 ./usr/share/lintian/overrides/python3-hisat2 +------------------------------------------------------------------------------+ | Post Build Thu, 09 Jul 2026 13:19:06 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 09 Jul 2026 13:19:06 +0000 | +------------------------------------------------------------------------------+ Purging /build/hisat2-jwYPXf Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 09 Jul 2026 13:19:07 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 125684 Build-Time: 393 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 13 Job: /srv/debomatic/incoming/hisat2_2.2.1-5.dsc Machine Architecture: amd64 Package: hisat2 Package-Time: 418 Source-Version: 2.2.1-5 Space: 125684 Status: successful Version: 2.2.1-5 -------------------------------------------------------------------------------- Finished at 2026-07-09T13:19:05Z Build needed 00:06:58, 125684k disk space