asivache 9eb38c0222 mostly synchronizing with the main branch. Based on anecdotal evidence (too few examples in the data), realignment (shifting indel left across a repeat) works correctly on non-homonucleotide repeats ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@928 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-07 16:39:16 +00:00
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gatk	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00
playground	mostly synchronizing with the main branch. Based on anecdotal evidence (too few examples in the data), realignment (shifting indel left across a repeat) works correctly on non-homonucleotide repeats	2009-06-07 16:39:16 +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