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File bowtie.changes of Package bowtie

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Wed May 18 12:39:25 UTC 2022 - Dominique Leuenberger <dimstar@opensuse.org>

- Update to version 1.3.1:
  + Fixed an overflow issue in `bowtie-build` that would sometimes
    yield corrupt "large" (64-bit) indexes; the resulting index
    would sometimes cause `bowtie` to hang. Note: `bowtie2-build`
    does not have this issue.
  + Fixed an issue in `bowtie` causing XM:i SAM optional field to
    sometimes be off by 1 when using the `-m/-M` flags.
  + Fixed an issue that would sometimes cause deadlocks in `bowtie`
    when running multithreaded.
  + Fixed an issue causing build errors when compiling against
    a pre-C++11 standard.

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Thu Apr 22 08:46:19 UTC 2021 - Ferdinand Thiessen <rpm@fthiessen.de>

- Fixed SPEC file: Replaced broken URL

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Mon Sep 14 14:01:01 UTC 2020 - Christophe Giboudeaux <christophe@krop.fr>

- Update to 1.3.0:
  * Fixed an issue causing bowtie to report incorrect results
    when using a Bowtie 2 index.
  * New, more efficient implementation of --reorder for
    keeping SAM output lines in same order as input reads
  * Added -x parameter for specifying index. bowtie still
    supports specifying an index via positional parameter,
    but this behavior will be deprecated.
  * Migrated python scripts to python3.
  * Fully removed colorspace functionality.
  * Added support for compiling on ARM architectures.
  * Fixed an issue preventing bowtie from outputting newlines
    in --max and --un output files.
  * Fixed an issue causing alignment results to vary based
    on read names.
  * Fixed an issue preventing --no-unal from suppressing
    unmapped reads.
  * Removed dependence on some third-party libraries,
    simplifying the code and improving portability.
  * Fix an issue preventing bowtie from running with
    many threads on big-endian machines.
- Spec cleanup
- Enable aarch64 and disable ppc* and s390x.

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Tue May 12 16:32:03 UTC 2020 - Guillaume GARDET <guillaume.gardet@opensuse.org>

- aarch64 is not yet supported on Bowtie1. See:
  https://github.com/BenLangmead/bowtie/pull/13

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Thu Nov  7 19:50:41 UTC 2019 - Atri Bhattacharya <badshah400@gmail.com>

- Update to version 1.2.3:
  * Added support for reading and inspecting Bowtie 2 indexes.
    Bowtie 2 indexes can now be used with either Bowtie or Bowtie
    2.
  * Added support for building an index from a gzipped-compressed
    FASTA.
  * Fixed issue preventing bowtie from reporting repeated
    alignments when -M is specified.
  * Fixed issue with -F mode omitting final base of each read.
  * Fixed clipping of first letter of first read in batches after
    first.
  * Fixed an issue preventing bowtie wrapper script from finding
    indexes.
- New BuildRequires: tbb-devel.
- Fix env based hashbangs.
- Use %%license to install LICENSE.
- Only build on 64-bit, building on 32-bit is no longer supported.

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Thu May  5 18:12:12 UTC 2016 - flyos@mailoo.org

- Initial release

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