@alexdobin alexdobin released this Aug 19, 2016 · 220 commits to master since this release

Assets 2
  • Fixed a problem with --outSAMmultNmax 1 not working for transcriptomic output.
  • Fixed a bug with chimeric BAM output for --chimOutType WithinBAM option.
  • Fixed a bug that could cause non-stable BAM sorting if the gcc qsort is unstable.
  • Fixed a bug with causing seg-faults when combining --twopassMode Basic --outSAMorder PairedKeepInputOrder .
  • Fixed a problem with SAM header in cases where reference sequences are added at the mapping stage.