File bowtie2.changes of Package bowtie2

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File bowtie2.changes of Package bowtie2 (Revision 5ebeb051280d6e00c202ecd15171452a)

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Wed Jan 18 05:31:26 UTC 2023 - Atri Bhattacharya <badshah400@gmail.com>

- Update to version 2.5.1:
  * Fixed an issue affecting bowtie2 alignment accuracy.
  * Updated the versions of the NCBI NGS and VDB libraries used by
    bowtie2.
  * Fixed a segmentation fault that would occur while aligning SRA
    data.
  * Fixed an issue preventing --un-mates from properly saving
    unaligned mates.

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Sun Nov 20 17:25:24 UTC 2022 - Atri Bhattacharya <badshah400@gmail.com>

- Update to version 2.5.0:
  * Overall improvements in the use of prefetch instructions.
  * Made input/output fully asynchronous by using a dedicated
    thread.
  * Added support for AVX2 256-bit instructions with can be
    enabled by setting the SSE_AXV2 environment variable at
    compile time.
  * Fixed an issue causing bowtie2 to crash when processing ZSTD
    files with high compression ratios.
  * Changed the way that unique alignments are counted in summary
    message to better match up with filters on SAM output.

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Thu Jan 20 19:38:08 UTC 2022 - Atri Bhattacharya <badshah400@gmail.com>

- Update to version 2.4.5:
  * Fixed issues with bowtie2 BAM parser that would cause bowtie2
    to crash when processing input that was encoded with tools
    other than samtools e.g. Picard.
  * Fixed an issue causing bowtie2 to drop certain optional fields
    when when aligning BAM reads with the --preserve-tags option.
  * Fixed an issue causing bowtie2 to produce mangled SAM output
    when specifying --sam-append-comment together with the
    --passthrough option.
  * Appended GO:query to SAM @HD entry to indicate that reads are
    grouped by query name, bump SAM version to 1.5 to indicate
    support for this change.
- Update simde to version 0.7.2.

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Fri Jul  2 23:48:10 UTC 2021 - Atri Bhattacharya <badshah400@gmail.com>

- Update to version 2.4.4:
  * Fixed an issue that would sometimes cause deadlocks in bowtie2
    when running multithreaded.

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Fri May 14 20:25:55 UTC 2021 - Atri Bhattacharya <badshah400@gmail.com>

- 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.

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Wed Oct 21 23:01:20 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>

- 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.

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Fri Oct 16 12:13:11 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>

- 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.

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Mon Jun 15 09:21:50 UTC 2020 - Pierre Bonamy <flyos@mailoo.org>

- Added bowtie2-processor_support.patch to fix GCC10 build fail
- Added %fdupes in the spec files to handle duplicated binary files

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Tue May 26 21:58:10 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>

- 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.

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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

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File bowtie2.changes of Package bowtie2 (Revision 5ebeb051280d6e00c202ecd15171452a)

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