107 Commits (a647f1e076a37d2fbfbbc7650a2111bcff74a367)

Author	SHA1	Message	Date
Eric Banks	62c5228048	1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method.	2012-07-17 12:23:40 -04:00
Eric Banks	40618ac471	A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots).	2012-07-17 10:52:43 -04:00
Eric Banks	f657b8bda8	Complete overhaul of the BQSRv2 integration tests. Much more comprehensive. Still need to deal with a few tests that need some modifications before I'm done, but I'll take care of that sometime tomorrow.	2012-07-17 00:32:34 -04:00
Eric Banks	52baac1e16	Move BQSRv2 into public and v1 into the archive.	2012-07-16 14:23:38 -04:00
Eric Banks	d7bf74fb7e	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
Mauricio Carneiro	6c17c50fa2	Updates to ReduceReads ... * Added optional parameter to not hard clip on the interval border * Made not clipping the default behavior (hence integration tests changed) * Updated integration tests.	2012-07-09 13:46:51 -04:00
Mauricio Carneiro	12d1c594df	Moving ReduceReads into protected	2012-06-25 17:01:33 -04:00