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File bowtie2.changes of Package bowtie2
------------------------------------------------------------------- Tue May 12 16:02:17 UTC 2020 - Guillaume GARDET <guillaume.gardet@opensuse.org> - Fix aarch64 build with: * simde sources * export POPCNT_CAPABILITY=0 ------------------------------------------------------------------- Sat Nov 30 02:16:08 UTC 2019 - Atri Bhattacharya <badshah400@gmail.com> - Use %%license to install LICENSE file. ------------------------------------------------------------------- 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. ------------------------------------------------------------------- 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. ------------------------------------------------------------------- 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 ------------------------------------------------------------------- Thu May 5 18:42:35 UTC 2016 - flyos@mailoo.org - Initial release
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