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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo 549293b6f7 Bugfixes towards final BCF2 implementation 
-- MLAC and MLAF in PoolCaller now use standard MLE_AC and MLE_AF
-- VCFDiffableReader disables onTheFly fixing of VCF header fields so comparisons are easier when headers are changing
-- Flag fields with FLAG_KEY=0 are parsed as though FLAG_KEY were entirely absent in AbstractVCFCodec to fix bug where FLAG_KEY=0 was being translated into FLAG_KEY in output VCF, making a false flag value a true one
-- Fix the GT field value in VariantContextTestProviders so it isn't fixed 1000s of times during testing
-- Keys whose value is null are put into the VariantContext info attributes now
 		2012-06-21 15:17:21 -04:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
gatk Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils Bugfixes towards final BCF2 implementation 2012-06-21 15:17:21 -04:00
BaseTest.java Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
MD5DB.java Finalizing BCF2 mark III commit 2012-06-21 15:16:27 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00