Mauricio Carneiro 0e93cf5297 Taking care of bad cigars in the GATK ... * fixed BadCigarFilter to filter out reads starting/ending in deletion and that have adjacent I/D events. * added Unit tests for BadCigarFilter * updated all exceptions in LocusIteratorByState to tell the user that he can instead run with -rf BadCigar * added the BadCigar filter to ReduceReads and RealignTargetCreator (if your walker blows up with these malformed reads, you may want to add it too)		2012-03-20 14:32:57 -04:00
..
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	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -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	GATK Report code cleanup	2012-03-19 11:53:57 -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	Fixing MD5's (new GATKReport header was missing from old md5's)	2012-03-19 15:28:45 -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