Changelog for
bowtie2-2.3.5.1-bp153.1.12.x86_64.rpm :
* 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
