Khalid Shakir b8b7f28aa9 Revving Picard to pick up new SamFileHeaderMerger. ... Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut(). In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124. - Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs. - Updated md5s to match new expectations after looking at TLEN diff engine output.		2012-05-02 16:47:28 -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	Revving Picard to pick up new SamFileHeaderMerger.	2012-05-02 16:47:28 -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	disabling all BQSR unit tests	2012-04-30 14:39:55 -04:00
BaseTest.java	Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow)	2012-04-03 18:55:52 -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	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00