asivache b48508a226 indelRealignment() signature changed. The only difference about consensus sequences is that they are passed along with alignment cigars that start inside the sequence, while for 'conventional' reads cigar always starts at position 0 on the read. Logically, indelRealignment() should not know what 'consensus' is. Instead, now it receives an additional int parameter, start of the cigar on the 'read' sequence ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@929 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-07 17:42:19 +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	indelRealignment() signature changed. The only difference about consensus sequences is that they are passed along with alignment cigars that start inside the sequence, while for 'conventional' reads cigar always starts at position 0 on the read. Logically, indelRealignment() should not know what 'consensus' is. Instead, now it receives an additional int parameter, start of the cigar on the 'read' sequence	2009-06-07 17:42:19 +00:00
test/org/broadinstitute/sting	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