Mauricio Carneiro 3b6e43b7c4 Use reads that span multiple intervals ... * RR will now compress reads that span across multiple intervals correctly and output them in the correct order. * Fixed bug in getReadCoordinateForReferenceCoordinate where if the requested reference coordinate fell inside a deletion in the read the read would be clipped up to one element past the deletion.		2011-09-27 18:39:06 -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	Use reads that span multiple intervals	2011-09-27 18:39:06 -04:00