Mark DePristo 11dbfc92a7 Horrible bugfix to decodeLoc() in BCF2Codec ... -- Just completely wrong. -- BCF2 shadowBCF now checks that the shadow bcf can be written to avoid /dev/null.bcf problem -- Added samtools ex2.bcf file for decoding to our integrationtests		2012-06-26 15:28:32 -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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	Update integration tests to reflect header changes	2012-06-26 15:28:32 -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	Horrible bugfix to decodeLoc() in BCF2Codec	2012-06-26 15:28:32 -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	Disable shadowBCF for VariantRecalibrationWalkers tests because it cannot handle symbolic alleles yet	2012-06-26 15:28:32 -04:00