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@alexdobin alexdobin released this Mar 17, 2017 · 462 commits to master since this release

  • Implemented --genomeFileSizes option to supply sizes of the genome index files. This allows for streaming of index files.

  • Implemented extra references input in the SAM/AM header from user-created "extraReferences.txt" file in the genome directory.

  • Implemented --chimOutType HardClip OR SoftClip options to output hard (default) / soft clipping in the BAM CIGAR for supplementary chimeric alignments.

  • Implemented --chimMainSegmentMultNmax parameters, which may be used to prohibit chimeric alignments with multimapping main segments to reduce false positive chimeras.

  • Implemented new SAM attribute 'ch' to mark chimeric aligmments in the BAM file for --chimOutType WithinBAM option.

  • Implemented --bamRemoveDuplicatesType UniqueIdenticalNotMulti option, which (unlike the UniqueIdentical optipon) will NOT mark multi-mappers as duplicates.

  • For --bamRemoveDuplicatesType UniqueIdentical, the unmmapped reads are no longer marked as duplicates.

  • Fixed occasional seg-faults after the completion of the mapping runs with shared memory.

  • Fixed a problem with RNEXT field in the Chimeric.out.sam file: RNEXT now always points to the other mate start.

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