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
..
bwa	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out	2010-01-02 20:19:14 +00:00
reference	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out	2010-01-02 20:19:14 +00:00
Aligner.java	Minor tweak to improve ease-of-use of iterator system.	2009-11-20 18:24:19 +00:00
Alignment.java	BWA: odds and ends. Get rid of some spurious debug code that was accidentally	2009-11-22 15:26:07 +00:00
AlignmentValidationWalker.java	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00
AlignmentWalker.java	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00
CountBestAlignmentsWalker.java	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00
package-info.java	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00