hanna c9a3707cfd Initial version of BWA/C bindings. Still lots of squirrels roaming the code. ... - Some cigar strings aren't right. - Memory leaks. - BWA codebase changes aren't committed to BWA tree. - Aligner interface butchered to support BWA/C-style alignments. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1928 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-28 21:37:49 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Initial version of BWA/C bindings. Still lots of squirrels roaming the code.	2009-10-28 21:37:49 +00:00
test/org/broadinstitute/sting	a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker	2009-10-26 20:18:55 +00:00