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Author SHA1 Message Date
Guillermo del Angel 40b8c7172c Pool Caller refactoring in preparation of GATK 2.0: a) PoolCallerUnifiedArgumentCollection disappeared, and arguments moved to UnifiedArgumentCollection. b) PoolCallerWalker is no longer needed and redundant, all functionality subsumed by UG. UG now checks if GATK is lite - if so, don't allow ploidy > 2. c) Moved pool classes from private to protected. d) Changed the way to specify ploidy. Instead of specifying samples per pool and having ploidy = 2*samplesPerPool, have user specify ploidy directly, which is cleaner. Update tests accordingly. We can now call triploid seedless grape genotypes correctly in theory. e) Renamed argument -reference to -reference_sample_calls since the former is ambiguous and it's not clear what it refers to. 2012-07-17 15:27:04 -04:00
Ryan Poplin bf2d5efe4d Moving HaplotypeCaller integration and unit tests over to protected as well. 2012-07-17 14:51:26 -04:00
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