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v1.2.2
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@ch4rr0 ch4rr0 released this 11 Dec 19:42
· 148 commits to master since this release
v1.2.2_p1
af3b677

Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (make NO_TBB=1).

  • Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems
  • Fixed major issue with incorrect alignment offsets being reported in --large-index mode
  • Fixed major issue with reads files being skipped when multiple inputs were specified together with -p/--threads
  • The official LICENSE of Bowtie was changed to Artistic License 2.0. This fixes an issue with the previous LICENSE, which mistakenly combined elements of different open-source licenses.
  • Fixed issue where bowtie would still run for a long time even when -u was set to a small number.
  • Fixed spurious "Reads file contained a pattern with more than 1024 quality values" error for some colorspace inputs.
  • Fixed issue with --strata sometimes failing to suppress alignments at lower strata.
  • Fixed issue with ends of paired-end reads sometimes appearing in non-adjacent lines of the SAM output with -p/--threads >1
  • Fixed issue whereby the read name of end #2 was not always truncated at the first whitespace character
  • Code simplifications
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