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- 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.