Mauricio Carneiro 56106d54ed Changing ReadUtils behavior to comply with GenomeLocParser ... Now the functions getRefCoordSoftUnclippedStart and getRefCoordSoftUnclippedEnd will return getUnclippedStart if the read is all contained within an insertion. Updated the contracts accordingly. This should give the same behavior as the GenomeLocParser now.		2011-09-19 14:00:00 -04:00
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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	Changing ReadUtils behavior to comply with GenomeLocParser	2011-09-19 14:00:00 -04:00