ebanks 64ac956885 Okay, I caved in: ... CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in. Thanks to Kiran this was pretty easy... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-30 00:32:26 +00:00
..
alignment	Fix bug where alignments with indels would be busted because bwa reverses	2009-10-29 21:33:13 +00:00
gatk	Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand.	2009-10-29 19:09:16 +00:00
playground	Okay, I caved in:	2009-10-30 00:32:26 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	-Mark just reminded me: actually force the ref/loc to be immutable	2009-10-29 13:41:53 +00:00