Mark DePristo 2f334a57c2 ReadGroupProperties mk2 ... -- Includes paired end status (T/F) -- Includes count of reads used in calculation -- Includes simple read type (2x76 for example) -- Better handling of insert size, read length when there's no data, or the data isn't paired end by emitting NA not 0		2012-03-01 18:43:53 -05:00
..
datasources	On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.	2012-02-13 12:35:09 -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	Revert "First implementation of GATKReportGatherer"	2012-02-08 23:28:55 -05:00
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	ReadGroupProperties mk2	2012-03-01 18:43:53 -05:00
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