Changelog for bowtie2-2.5.3-25.27.x86_64.rpm :

* Sat Feb 24 2024 Atri Bhattacharya - 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 - 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 - 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 - 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 - 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 AATTHD 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 - 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 - 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 - 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 - 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 - Added bowtie2-processor_support.patch to fix GCC10 build fail- Added %fdupes in the spec files to handle duplicated binary files