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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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
gatk	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00
jna	Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE	2011-08-23 23:49:36 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00
BaseTest.java	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
MD5DB.java	Go for global integrationtest path first, if possible.	2011-07-26 17:35:30 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00