Mark DePristo c3b8048e2e Moving around classes in VCF and BCF2 ... -- Refactored VCF writers into vcf.writers package -- Moved BCF2Writer to bcf2.writer -- Updates to all of the walkers using VCFWriter to reflect new packages -- A large number of files had their headers cleaned up because of this as well		2012-05-24 10:56:58 -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	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.	2012-05-21 15:41:56 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Moving around classes in VCF and BCF2	2012-05-24 10:56:58 -04:00
BaseTest.java	Revert bad part of last commit that shouldn't have been pushed	2012-05-10 10:41:08 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00