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| Name: bowtie2 | Distribution: openSUSE:Factory:zSystems |
| Version: 2.5.2 | Vendor: openSUSE |
| Release: 1.1 | Build date: Sat Oct 21 16:48:54 2023 |
| Group: Productivity/Scientific/Other | Build host: s390zl23 |
| Size: 4746463 | Source RPM: bowtie2-2.5.2-1.1.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| Summary: Fast and memory-efficient short read aligner | |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
GPL-3.0-only
* Thu Oct 19 2023 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.5.2:
* Fixed an issue preventing bowtie2 from utilizing the specified
number of CPU cores.
* Fixed an issue causing bowtie2 to segfault while parsing
interleaved reads.
* Overhauled the FASTQ parser with better tolerance for empty
lines.
- Update simde to version 0.7.6.
- Allow building with LTO, do not set _lto_cflags to %{nil}.
* Wed Jan 18 2023 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.5.1:
* Fixed an issue affecting bowtie2 alignment accuracy.
* Updated the versions of the NCBI NGS and VDB libraries used by
bowtie2.
* Fixed a segmentation fault that would occur while aligning SRA
data.
* Fixed an issue preventing --un-mates from properly saving
unaligned mates.
* Sun Nov 20 2022 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.5.0:
* Overall improvements in the use of prefetch instructions.
* Made input/output fully asynchronous by using a dedicated
thread.
* Added support for AVX2 256-bit instructions with can be
enabled by setting the SSE_AXV2 environment variable at
compile time.
* Fixed an issue causing bowtie2 to crash when processing ZSTD
files with high compression ratios.
* Changed the way that unique alignments are counted in summary
message to better match up with filters on SAM output.
* Thu Jan 20 2022 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.4.5:
* Fixed issues with bowtie2 BAM parser that would cause bowtie2
to crash when processing input that was encoded with tools
other than samtools e.g. Picard.
* Fixed an issue causing bowtie2 to drop certain optional fields
when when aligning BAM reads with the --preserve-tags option.
* Fixed an issue causing bowtie2 to produce mangled SAM output
when specifying --sam-append-comment together with the
- -passthrough option.
* Appended GO:query to SAM @HD entry to indicate that reads are
grouped by query name, bump SAM version to 1.5 to indicate
support for this change.
- Update simde to version 0.7.2.
* Fri Jul 02 2021 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.4.4:
* Fixed an issue that would sometimes cause deadlocks in bowtie2
when running multithreaded.
* Fri May 14 2021 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.4.3:
* Replaced TBB concurrency with C++ threads.
* Added native support for processing Zstd-compressed read files
to bowtie2.
* Added native support for processing Zstd-compressed
reference-genome files to bowtie2-build.
* Fixed an issue causing `bowtie2` to report incorrect
alignments on big-endian machines.
* Fixed an issue causing `bowtie2` to incorrectly process BAM
files on big-endian machines.
* Fixed an issue causing Bowtie2 to set an incorrect MAPQ when
AS and XS are the maximum for read length.
* Add support for building on Apple M1 processors.
- Update simde to version 0.7.0.
- Drop BuildRequires tbb-devel: no longer required.
- RelWithDebInfo isn't supported and assumes fully unoptimised
Debug mode; use Release mode instead by passing
`-DCMAKE_RELEASE_TYPE=Release` to cmake.
* Wed Oct 21 2020 Atri Bhattacharya <badshah400@gmail.com>
- Actually update bowtie2 source to version 2.4.2 (fixing previous
revision).
- Drop patches incorporated upstream:
* bowtie2-processor_support.patch (commit ebb07cf).
* bowtie2-cmake-install-targets.patch (commit c9d92ce).
- Package README.md file as doc.
* Fri Oct 16 2020 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.4.2:
* Fixed an issue that would cause the `bowtie2` wrapper script
to throw an error when using wrapper-specific arguments.
* Added new `--sam-append-comment` flag that appends comment
from FASTA/Q read to corresponding SAM record.
* Fixed an issue that would cause qupto, `-u`, to overflow when
there are >= 2^32 query sequences
(gh#BenLangmead/bowtie2#312).
* Fixed an issue that would cause bowtie2-build script to
incorrectly process reference files.
- Drop _service file and use tagged version of simde instead (at
version 0.6.0); correspondingly drop the obsinfo and obscpio
files as well.
* Mon Jun 15 2020 Pierre Bonamy <flyos@mailoo.org>
- Added bowtie2-processor_support.patch to fix GCC10 build fail
- Added %fdupes in the spec files to handle duplicated binary files
* Tue May 26 2020 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.4.1:
* Fixed an issue that would cause the bowtie2 wrapper script to
incorrectly process certain arguments.
- Changes from version 2.4.0:
* Fixed an issue in BAM pattern source where one thread would
prematurely close the read file pointer resulting in other
threads crashing because of "Bad file descriptor" errors.
* Fixed an issue that would cause bowtie2 to crash with
`--no-1mm-upfront` specified.
* Modified bowtie2-build script to better handle of flags and
positional parameters.
* Migrated all python scripts to python3.
* Added support for wildcards in input files to bowtie2 wrapper
script e.g. `bowtie2 -x index -q *.fq` as opposed to `bowtie2
- x index -q 1.fq,2.fq,3.fq...`.
* Fixed an issue causing bowtie2 to incorrectly process read
names see [gh#BenLangmead/bowtie2#265].
* Added support for allowing presets to be overridden by more
specific options e.g `bowtie2 -x index --local
- -very-fast-local --L22 -q reads.fq` will cause bowtie2 to use
a seed length of 22 instead of a seed length of 25 that's
configured for `--very-fast-local` preset.
* Modified SAM output for `-k`/`-a` so that supplementary
alignments get assigned a MAPQ of 255.
* Fixed an issue that would cause bowtie2-build to not generate
reverse index files.
* Added preliminary support for ppc64le architectures with the
help of SIMDE project see [gh#BenLangmead/bowtie2#271] for
details.
* Fixed an issue causing bowtie2 to incorrectly calculate the
MAPQ when `--mp` was specified in combination with
`--ignore-quals`.
- Add bowtie2-cmake-install-targets.patch to fix cmake scripts,
specfically adding install targets and fixing tests (still does
not work) [gh#BenLangmead/bowtie2#292].
- Use cmake for building (BuildRequires: cmake); adapt
appropriately for aarch64.
- Use pkgconfig based BuildRequires for zlib.
* Tue May 12 2020 Guillaume GARDET <guillaume.gardet@opensuse.org>
- Fix aarch64 build with:
* simde sources
* export POPCNT_CAPABILITY=0
/usr/bin/bowtie2 /usr/bin/bowtie2-align-l /usr/bin/bowtie2-align-s /usr/bin/bowtie2-build /usr/bin/bowtie2-build-l /usr/bin/bowtie2-build-s /usr/bin/bowtie2-inspect /usr/bin/bowtie2-inspect-l /usr/bin/bowtie2-inspect-s /usr/share/doc/packages/bowtie2 /usr/share/doc/packages/bowtie2/AUTHORS /usr/share/doc/packages/bowtie2/BOWTIE2_VERSION /usr/share/doc/packages/bowtie2/MANUAL /usr/share/doc/packages/bowtie2/NEWS /usr/share/doc/packages/bowtie2/README.md /usr/share/doc/packages/bowtie2/TUTORIAL /usr/share/licenses/bowtie2 /usr/share/licenses/bowtie2/LICENSE
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