ebanks 772f558ae0 Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code. ... Small change for Ryan to get hard-clipped reads working for the recalibrator. PLEASE DO NOT RELEASE THIS WEEK. I still have some more testing to do and need Mark to run WG jobs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-25 20:04:33 +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	Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.	2010-05-25 20:04:33 +00:00
test/org/broadinstitute/sting	a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated.	2010-05-21 22:25:17 +00:00