hanna 665951f9f0 Support negative strand alignments. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1748 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-30 18:10:26 +00:00
..
bwt	More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes.	2009-09-23 23:44:59 +00:00
packing	Time for a reorganization. Repackage generally useful alignment classes lower in the package structure, and create a subpackage for bwa-specific code. Repackage BWA alignment code away from BWT representation. Isolate byte- and word-packing streams in another package that will ultimately be killed off en masse.	2009-09-17 23:28:47 +00:00
AlignerTestHarness.java	Support negative strand alignments.	2009-09-30 18:10:26 +00:00
AlignmentState.java	Indels supported. Variable gap penalties are not yet taken into account.	2009-09-24 21:03:02 +00:00
BWAAligner.java	Support negative strand alignments.	2009-09-30 18:10:26 +00:00
BWAAlignment.java	Start of refactoring effort. Make construction of alignment object simpler.	2009-09-30 15:19:31 +00:00
LowerBound.java	Support 'N's and other mismatch characters in the reference.	2009-09-24 21:41:30 +00:00