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| Name: bowtie2 | Distribution: openSUSE Leap 16.0 |
| Version: 2.5.4 | Vendor: openSUSE |
| Release: lp160.1.1 | Build date: Wed Aug 7 08:09:40 2024 |
| Group: Productivity/Scientific/Other | Build host: reproducible |
| Size: 4742136 | Source RPM: bowtie2-2.5.4-lp160.1.1.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
* Wed Aug 07 2024 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.5.4:
* Added --sam-opt-config command line option for toggling SAM
Opt flags.
* Fixed an issue causing bowtie2’s memory usage to increase over
time when aligning BAM files.
* Changed bowtie2 to continue flushing output in the event of a
partial write.
* Changed the behavior of bowtie2-build to throw an exception if
it is unable to write the BWT (.1.bt2, .1.rev.bt2). In prior
versions bowtie2-build, would silently ignore the error which
has led some to report the absence of the BWT files in a
“completed” index build.
* Reverted the changes made in v2.5.0 that sometimes caused
unique concordant alignments to be overcounted.
* Sat Feb 24 2024 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.5.3:
* Fixed an issue causing bowtie2's memory usage to increase over
time.
* Fixed an issue causing bowtie2 to crash when processing empty
FASTQ records.
* Fixed an issue that would cause bowtie2 to erroneously treat
- f and -F as mutually exclusive.
* Add optional support for libsais to bowtie2-build for faster
index building.
* 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
* Sat Nov 30 2019 Atri Bhattacharya <badshah400@gmail.com>
- Use %%license to install LICENSE file.
* Thu Nov 07 2019 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.3.5.1:
* Added official support for BAM input files.
* Added official support for CMake build system.
* Added changes to Makefile for creating Reproducible builds
[gh#BenLangmead/bowtie2#210].
* Fix an issue whereby building on aarch64 would require
patching sed commands [gh#BenLangmead/bowtie2#243].
* Fix an issue whereby `bowtie2` would incorrectly throw an
error while processing `--interleaved` input.
- Changes from version 2.3.5:
* Added support for obtaining input reads directly from the
Sequence Read Archive, via NCBI's [NGS language
bindings](https://github.com/ncbi/ngs). This is activated via
the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc)
option. This implementation is based on Daehwan Kim's in
[HISAT2](https://ccb.jhu.edu/software/hisat2). Supports both
unpaired and paired-end inputs.
* Bowtie 2 now compiles on ARM architectures (via
[gh#BenLangmead/bowtie2#216].
* `--interleaved` can now be combined with FASTA inputs (worked
only with FASTQ before).
* Fixed issue whereby large indexes were not successfully found
in the `$BOWTIE2_INDEXES` directory.
* Fixed input from FIFOs (e.g. via process substitution) to
distinguish gzip-compressed versus uncompressed input.
* Fixed issue whereby arguments containing `bz2` `lz4` were
misinterpretted as files.
* Fixed several compiler warnings.
* Fixed issue whereby both ends of a paired-end read could have
negative TLEN if they exactly coincided
* Fixed issue whereby `bowtie2-build` would hang on end-of-file
[gh#BenLangmead/bowtie2#228].
* Fixed issue whereby wrapper script would sometimes create
zombie processes [gh#BenLangmead/bowtie2#51].
* Fixed issue whereby `bowtie2-build` and `bowtie2-inspect`
wrappers would fail on some versions of Python/PyPy.
* Replaced old, unhelpful `README.md` in the project with a
version that includes badges, links and some highlights from
the manual.
* Wed Feb 28 2018 badshah400@gmail.com
- Update to version 2.3.4.1:
* Fixed an issue with --reorder that caused bowtie2 to crash
while reordering SAM output
- Changes from version 2.3.4:
* Fixed major issue causing corrupt SAM output when using many
threads (-p/--threads) on certain systems.
* Fixed an issue whereby bowtie2 processes could overwrite each
others' named pipes on HPC systems.
* Fixed an issue causing bowtie2-build and bowtie2-inspect to
return prematurely on Windows.
* Fixed issues raised by compiler "sanitizers" that could
potentially have caused memory corruption or undefined
behavior.
* Added the "continuous FASTA" input format (-F) for aligning
all the k-mers in the sequences of a FASTA file. Useful for
determining mapability of regions of the genome, and similar
tasks.
- Run sed on binaries to modify env based hashbangs to ones that
directly call executables.
- Drop bowtie2-gcc6.patch; incorporated upstream.
* Mon Sep 04 2017 mpluskal@suse.com
- Update to version 2.3.2:
* Added support for interleaved paired-end FASTQ inputs
(--interleaved)
* Now reports MREVERSE SAM flag for unaligned end when only one
end of a pair aligns
* Fixed issue where first character of some read names was
omitted from SAM output when using tabbed input formats.
* Added --sam-no-qname-trunc option.
* Fixed compilation error caused by pointer comparison issue in aligner_result.cpp
* Removed termcap and readline dependencies introduced in v2.3.1
* Fixed compilation issues caused by gzbuffer function when
compiling with zlib v1.2.3.5 and earlier.
* Fixed issue that would cause Bowtie 2 hang when aligning FASTA
inputs with more than one thread
- Changes for version 2.3.0:
* Code related to read parsing was completely rewritten to improve
scalability to many threads.
* TBB is now the default threading library.
* Bowtie now uses a queue-based lock rather than a spin or
heavyweight lock.
* Unnecessary thread synchronization removed
* Fixed issue with parsing FASTA records with greater-than symbol
in the name
* Changed default for --bmaxdivn to yield better memory footprint
and running time when building an index with many threads
- Add bowtie2-gcc6.patch (fixes compilation with gcc6+)
- Build using optflags
- Update download url
- Small package cleanup with spec-cleaner
* Thu May 05 2016 flyos@mailoo.org
- Initial release
/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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