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v1.2.1
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@ch4rr0 ch4rr0 released this 12 Jun 20:50
· 212 commits to master since this release
v1.2.1
f524981

Please note that Bowtie will be switching to the Artistic 2.0 license in the next release.
Pre-build binaries now include statically linked TBB and zlib libraries no longer requiring
these libraries to be pre-installed

  • Fixed an issue which caused Bowtie to hang during parallell index building when running an optimized binary
  • Deprecated --refout option. It will be fully removed in the next release
  • Added parallel index building with the bowtie2-build --threads option (credit to Aidan Reilly - https://github.com/aidanreilly8)
  • Added native support for gzipped read files. The wrapper script is no longer responsible for this, which simplifies the wrapper and improves speed and thread scaling.
  • Added support for interleaved paired-end FASTQ inputs (--interleaved)
  • Fixed issue where first character of some read names was omitted from SAM output when using tabbed input formats
  • Fixed issue that caused Bowtie to hang when aligning FASTA inputs with more than one thread
  • Bowtie wrapper now works even when invoked via a symlink in a different directory from the executables
  • Fixed issue preventing reading --tab5 input on stdin
  • Added --no-unal option for suppressing unmapped reads in SAM output
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