- Update to version 2.4.4: * Fixed an issue that would sometimes cause deadlocks in bowtie2 when running multithreaded.
- 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.
- 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.
- 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.
- Added bowtie2-processor_support.patch to fix GCC10 build fail - Added %fdupes in the spec files to handle duplicated binary files
- 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.
- Fix aarch64 build with: * simde sources * export POPCNT_CAPABILITY=0
- Use %%license to install LICENSE file.
- Update to version 22.214.171.124: * 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.
- Update to version 126.96.36.199: * 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.
- 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 v188.8.131.52 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
- Initial release