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Revisions of bowtie

buildservice-autocommit accepted request 977947 from Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) (revision 11) 
baserev update by copy to link target
buildservice-autocommit accepted request 887524 from Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) (revision 9) 
baserev update by copy to link target
buildservice-autocommit accepted request 834334 from Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) (revision 7) 
baserev update by copy to link target
Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) accepted request 834329 from Christophe Giboudeaux's avatar Christophe Giboudeaux (cgiboudeaux) (revision 6) 
- 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.
buildservice-autocommit accepted request 803351 from Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) (revision 5) 
baserev update by copy to link target
Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) accepted request 803243 from Guillaume GARDET's avatar Guillaume GARDET (Guillaume_G) (revision 4) 
- aarch64 is not yet supported on Bowtie1. See:
  https://github.com/BenLangmead/bowtie/pull/13
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 746521 from Ana Guerrero's avatar Ana Guerrero (anag) (revision 3) 
initialized devel package after accepting 746521
Ana Guerrero's avatar Ana Guerrero (anag) accepted request 746517 from Atri Bhattacharya's avatar Atri Bhattacharya (badshah400) (revision 2) 
- 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.
Matthias Mailänder's avatar Matthias Mailänder (Mailaender) accepted request 397076 from Pierre Bonamy's avatar Pierre Bonamy (flyos) (revision 1) 
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
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