b7511c5ff3
-- 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 |
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