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