ebanks 4678613893 Significant fixes for the Genomic Annotator. ... 1. Rip out all of Ben's code intended to circumvent the stable VCF Writer output system in multi-threaded mode (I threw up a little when I saw this code). This will improve memory consumption when running with -nt. 2. Don't annotate indels or > bi-allelic sites. 3. Fix bug where not all records were making it into the output VCF. 4. General code clean up. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4118 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-25 20:16:50 +00:00
..
alignment	Disabled AlignerIntegrationTest while addressing build machine memory issues.	2010-08-14 01:23:21 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	GenerateVariantClusters and VariantRecalibrator now uses hapmap and 1kg ROD bindings (in addition to dbsnp) to distinguish between knowns and novels. It no longer looks at by-hapmap validation status so providing hapmap is highly recommended. Example on the wiki. Input variants tracks now must start with input.	2010-08-25 18:33:40 +00:00
oneoffprojects/walkers	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
playground	Significant fixes for the Genomic Annotator.	2010-08-25 20:16:50 +00:00
utils	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
BaseTest.java	Moving pointer to b36 reference from /broad/1KG to /humgen/1kg	2010-08-13 00:54:34 +00:00
WalkerTest.java	remove testing code from tribble track builder, set the command line program in walker test to null to reclaim memory in integration tests, and removed some orphaned intergration tests.	2010-08-16 23:52:01 +00:00