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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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	getRefCoordSoftUnclippedStart and End refactor	2011-12-20 17:48:51 -05:00
test	getRefCoordSoftUnclippedStart and End refactor	2011-12-20 17:48:51 -05:00