Changelog for bowtie2-2.5.3-bp156.25.14.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
* Tue May 26 2020 Atri Bhattacharya - 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 - Fix aarch64 build with:
* simde sources
* export POPCNT_CAPABILITY=0
* Sat Nov 30 2019 Atri Bhattacharya - Use %%license to install LICENSE file.
* Thu Nov 07 2019 Atri Bhattacharya - 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 badshah400AATTgmail.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 mpluskalAATTsuse.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 flyosAATTmailoo.org- Initial release