ab53220635
* Sites with more soft clipped bases than regular will force-trigger a variant region * No more unclipping/reclipping, RR machinery now handles soft clips natively. * implemented support for base insertion and base deletion quality scores in synthetic and regular reads. * GATKSAMRecord clone() now creates a fresh object for temporary attributes if one is present. note: SAMRecords create a shallow copy of the tempAttribute object which was causing multiple reads (that came from the same read) to have their temporary attributes modified by one another inside reduce reads. Beware, if you're not using GATKSAMRecord! |
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