File bowtie2.changes of Package bowtie2

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File bowtie2.changes of Package bowtie2 (Revision 30740f21760a06406402979493de2cb7)

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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

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