File bowtie2.changes of Package bowtie2
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Fri Mar 21 00:48:31 UTC 2025 - Shawn Dunn <sfalken@opensuse.org>
- Add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to fix FTBFS with cmake4
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Wed Aug 7 06:09:40 UTC 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.
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Sat Feb 24 17:35:38 UTC 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.
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Thu Oct 19 12:32:32 UTC 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}.
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Wed Jan 18 05:31:26 UTC 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.
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Sun Nov 20 17:25:24 UTC 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.
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Thu Jan 20 19:38:08 UTC 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.
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Fri Jul 2 23:48:10 UTC 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.
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Fri May 14 20:25:55 UTC 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.
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Wed Oct 21 23:01:20 UTC 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.
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Fri Oct 16 12:13:11 UTC 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.
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Mon Jun 15 09:21:50 UTC 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
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Tue May 26 21:58:10 UTC 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.
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Tue May 12 16:02:17 UTC 2020 - Guillaume GARDET <guillaume.gardet@opensuse.org>
- Fix aarch64 build with:
* simde sources
* export POPCNT_CAPABILITY=0
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Sat Nov 30 02:16:08 UTC 2019 - Atri Bhattacharya <badshah400@gmail.com>
- Use %%license to install LICENSE file.
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Thu Nov 7 20:11:08 UTC 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.
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Wed Feb 28 13:14:53 UTC 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.
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Mon Sep 4 10:17:15 UTC 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
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Thu May 5 18:42:35 UTC 2016 - flyos@mailoo.org
- Initial release
