asivache df2a7039cb Henious bug fixed: only rookies forget that external conditions need to be re-checked after loop ends on some other condition, duh! In addition, msa piles are now seeded with a single read sequence each (if there are less then 4 reads it might be hard to seed with two pairs) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@129 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-21 18:32:18 +00:00
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src/org/broadinstitute/sting	Henious bug fixed: only rookies forget that external conditions need to be re-checked after loop ends on some other condition, duh! In addition, msa piles are now seeded with a single read sequence each (if there are less then 4 reads it might be hard to seed with two pairs)	2009-03-21 18:32:18 +00:00