Mark DePristo 24864fd5b0 GATK now writes BCF output to any file with .bcf extension ... -- Moved VCF and BCF writers to variantcontext.writers -- Updated vcf.jar build path -- Refactored VCFWriter and other code. Now the best (and soon to be only) way to create these files is through a factory method called VariantContextWriterFactory. Renamed the general VCFWriter interface to VariantContextWriter which is implemented by VCFWriter and BCF2Writer.		2012-05-24 10:57:00 -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	GATK now writes BCF output to any file with .bcf extension	2012-05-24 10:57:00 -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	…
WalkerTest.java	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00