Mauricio Carneiro 5bba44d693 Added hardClipByReferenceCoordinates UnitTest for the ReadClipper ... * fixed edge case when requested to hard clip beginning of a read that had hanging soft clipped bases on the left tail. * fixed edge case when requested to hard clip end of a read that had hanging soft clipped bases on the right tail. * fixed AlignmentStart of a clipped read that results in only hard clips and soft clips note: added tests to all these beautiful cases...		2011-12-16 18:01:33 -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	Added hardClipByReferenceCoordinates UnitTest for the ReadClipper	2011-12-16 18:01:33 -05:00