depristo 57a13805da GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3596 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-19 21:36:41 +00:00
..
arguments	First pass at eliminating the old sharding system. Classes required for the original sharding system	2010-06-17 20:17:31 +00:00
contexts	Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept	2010-06-13 01:47:02 +00:00
datasources	Merging the sharding-specific inherited classes down into the base.	2010-06-17 22:36:13 +00:00
examples	Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes	2010-02-05 21:47:54 +00:00
executive	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
filters	Re-allowing blacklist by read group id.	2010-06-16 19:45:44 +00:00
io	Fixed UG parallelization bug. Better integration test to catch this in the future.	2010-05-25 21:03:45 +00:00
iterators	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
refdata	GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.	2010-06-19 21:36:41 +00:00
traversals	Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept	2010-06-13 01:47:02 +00:00
walkers	Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval.	2010-06-18 21:51:40 +00:00
CommandLineExecutable.java	Better error message when bam file / list file with wrong extension is	2010-06-03 17:52:48 +00:00
CommandLineGATK.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
DownsampleType.java	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
DownsamplingMethod.java	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
GATKErrorReport.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
GenomeAnalysisEngine.java	Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.	2010-06-18 17:37:11 +00:00
Reads.java	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +00:00
WalkerManager.java	Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:	2010-05-28 14:52:44 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00