hanna f37564e63a Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1817 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-13 15:50:04 +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	Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C.	2009-10-13 15:50:04 +00:00
AlignmentMatchSequence.java	Fixed 'visualization' of reads that didn't match bwa's alignments exactly.	2009-10-08 19:45:30 +00:00
AlignmentState.java	Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x.	2009-10-03 21:55:18 +00:00
BWAAligner.java	Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C.	2009-10-13 15:50:04 +00:00
BWAAlignment.java	Fixed 'visualization' of reads that didn't match bwa's alignments exactly.	2009-10-08 19:45:30 +00:00
LowerBound.java	Support 'N's and other mismatch characters in the reference.	2009-09-24 21:41:30 +00:00