Mauricio Carneiro d561914d4f Revert "First implementation of GATKReportGatherer" ... premature push from my part. Roger is still working on the new format and we need to update the other tools to operate correctly with the new GATKReport. This reverts commit aea0de314220810c2666055dc75f04f9010436ad.		2012-02-08 23:28:55 -05:00
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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	Revert "First implementation of GATKReportGatherer"	2012-02-08 23:28:55 -05:00
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	make the size of a GenomeLoc int instead of long	2012-02-03 17:12:42 -05:00
BaseTest.java	Refactor the Pileup Element with regards to indels	2012-01-24 16:07:21 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00