Mauricio Carneiro 389380a590 ReduceReads ref bases are now output as '=' to save space ... Restructured the sliding window framework to manipulate a wrapped version of the SAMRecord that contains information about the reference.		2011-10-30 12:04:39 -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	ReduceReads ref bases are now output as '=' to save space	2011-10-30 12:04:39 -04:00