asivache d5cd883b99 bug fixed when a read with alignment end exactly at the window boundary and with last cigar element being an indel would cause index-out-of-bounds exception ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@992 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-11 21:03:15 +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	bug fixed when a read with alignment end exactly at the window boundary and with last cigar element being an indel would cause index-out-of-bounds exception	2009-06-11 21:03:15 +00:00
test/org/broadinstitute/sting	First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.	2009-06-11 20:18:13 +00:00