depristo 0f43b10c39 Optimization in CombineVariants when merging into a sites_only VCF ... VariantContextUtils now was a utility function that creates a sitesOnlyVariantContext from an input VC Add complex merge test of SNPs and indels from the new batch merge wiki in : http://www.broadinstitute.org/gsa/wiki/index.php/Merging_batched_call_sets with multiple alleles for an indel. Created a BatchMergeIntegrationTest that uses GGA with the complex merged input alleles to genotype SNPs and Indels with multiple alleles simultaneously in NA12878. Looks great. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5959 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-08 14:31:46 +00:00
..
alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	Optimization in CombineVariants when merging into a sites_only VCF	2011-06-08 14:31:46 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods.	2011-05-23 18:06:05 +00:00
playground/gatk/walkers	More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.	2011-06-03 20:11:31 +00:00
utils	No one should be calling the createHeader method(s) directly, but instead should be going through the full readHeader method (because it first sets the version); therefore I made them package protected and merged them. Updated the various unit tests that were using createHeader and were dangerously assuming that the header version was defaulting to 4.0 (which it no longer does).	2011-06-03 02:17:37 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	The previous version of the UG was always creating BAQ'd pileups for the underlying site QUAL calculation. This resulted in some slowdown in the code. But as far as I can tell, the code actually didn't apply the BAQ'd base quality anywhere when the BAQ field wasn't in the read, so this just saves us 20% of the runtime when BAQ isn't enabled from heading into the BAQ subsystem when we don't actually want to get the BAQ'd base qualities.	2011-05-27 14:00:52 +00:00