asivache b4ef16ced2 extractIndels() now should deal correctly with soft- and hard-clipped bases ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@936 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-08 16:04:49 +00:00
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gatk	added support for the -M option in traversals.	2009-06-08 15:12:24 +00:00
playground	extractIndels() now should deal correctly with soft- and hard-clipped bases	2009-06-08 16:04:49 +00:00
secondarybase	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
utils	added sequencePeriod(String seq, int minPeriod) - finds smallest period equal to or greater than minPeriod for the specified text string seq; this is a trivial (hopefully correct) back-of-the-envelope implementation for a well-known and well-studied problem; there should be more efficient algorithms in the wild	2009-06-06 23:05:24 +00:00