depristo 9cc808104e Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers. ... Also cleaned up the debugging output. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@432 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-15 19:08:26 +00:00
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src/org/broadinstitute/sting	Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers.	2009-04-15 19:08:26 +00:00
test/org/broadinstitute/sting	Added a bunch of changes to support the new MicroManager code	2009-04-15 18:29:38 +00:00