rpoplin 9cbae53ee1 Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2548 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-08 15:19:22 +00:00
..
alignment	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out	2010-01-02 20:19:14 +00:00
gatk	Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity.	2010-01-08 15:19:22 +00:00
playground/gatk/walkers	Fixed broken test	2010-01-08 06:13:01 +00:00
utils	Minor interface change for VCFGenotypeRecord.	2010-01-07 16:48:09 +00:00
BaseTest.java	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.	2009-11-24 02:34:48 +00:00