hanna b6ecc9e151 Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out ... and the data backing it up deleted without my knowledge. Unfortunately, since the data was deleted, I had to regenerate the data and a new md5. Hopefully the aligner output is still correct. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-02 20:19:14 +00:00
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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	Now that we changed how deletions are represented, got to update MD5...	2009-12-30 22:00:58 +00:00
playground/gatk/walkers	forgot to update md5s	2009-12-29 20:31:29 +00:00
utils	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +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