hanna b0ec7fc144 More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes. ... Limitations: 1) Can't handle RC alignments. 2) Can't handle indels. 3) Can't handle N's in reference bases. 4) Stops at first hit. Ran BWT over a test suite of 800k Ecoli reads. After removing alignments with indels / reads with Ns, the remaining reads were aligned with quality 'equal to' that of the alignment stored in the BAM file. In this case 'equal' quality is <= mismatches to the reference as the existing alignment stored in the BAM file. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1710 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-23 23:44:59 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes.	2009-09-23 23:44:59 +00:00
test/org/broadinstitute/sting	a couple of light changes to GenomeLocSortedSet.	2009-09-23 20:38:53 +00:00