splice-bam.groovy must remove soft-clips in aligned contigs

nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.

GNU Lesser General Public License v3.0

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Closed ckennedy-nmdp closed 9 years ago

ckennedy-nmdp commented 9 years ago

Otherwise the region-coordinates will have the wrong sequence offset (equal to the soft-clip). Treat the CIGAR value "S" as a "D".

ghost commented 9 years ago

Fixed by #86