Fixed the header of the Log.progress.out. --sjdbFileChrStartEnd can now accept multiple files which will be concatenated. Added --outSAMflagOR, --outSAMflagAND options to set specific bits of the SAM FLAG. Fixed wrong output of chimeric junctions boundaries in the Chimeric.out.junction file. Added --alignSoftClipAtReferenceEnds No option which prevents soft clipping of alignments at the reference (chromosome) ends, for compatibility with Cufflinks/cuffmerge.
Fixed a bug with output score (AS attribute) of some chimeric alignments.
2.4.0g
STAR_2.4.0g