Mauricio Carneiro 7532be7f5a Allowing to clip after AlignmentEnd if end is soft clipped. ... Read clipper now identifies and clips even if the requested coordinate is outside the alignment but the read contains soft clipped bases in that region.		2011-08-30 02:44:46 -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	Allowing to clip after AlignmentEnd if end is soft clipped.	2011-08-30 02:44:46 -04:00