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
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bqsr	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
compression/reducereads	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
genotyper	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
haplotypecaller	Moving HaplotypeCaller integration and unit tests over to protected as well.	2012-07-17 14:51:26 -04:00