Mark DePristo b7511c5ff3 Fixed long-standing bug in tribble index creation ... -- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write -- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index -- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils -- VCFWriter now requires the master sequence dictionary -- Updated walkers that create VCFWriters to provide the master sequence dictionary		2011-09-20 10:53:18 -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	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00