Mauricio Carneiro cadff40247 getRefCoordSoftUnclippedStart and End refactor ... These functions are methods of the read, and supplement getAlignmentStart() and getUnclippedStart() by calculating the unclipped start counting only soft clips. * Removed from ReadUtils * Added to GATKSAMRecord * Changed name to getSoftStart() and getSoftEnd * Updated third party code accordingly.		2011-12-20 17:48:51 -05:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	getRefCoordSoftUnclippedStart and End refactor	2011-12-20 17:48:51 -05:00