Mauricio Carneiro 0d4ea30d6d Updating the BQSR Gatherer to the new file format ... This is important for quick turnaround in the analysis cycle of the new covariates. Also added a dummy unit test that doesn't really test anything (disabled), but helps in debugging.		2012-03-19 09:02:27 -04:00
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datasources	Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices	2012-03-08 15:30:44 -05:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these.	2012-02-25 13:57:28 -05:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	GATKReport v1.0	2012-03-12 23:09:19 -04:00
samples	Added UnitTests for getFamilies() and getChildrenWithParents()	2011-12-09 15:57:07 +01:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Updating the BQSR Gatherer to the new file format	2012-03-19 09:02:27 -04:00
EngineFeaturesIntegrationTest.java	Bugfix for incorrect error messages for missing BAMs and VCFs	2012-01-23 09:52:07 -05:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00