Mark DePristo cc8c12b954 Committing a broken version of BaseRecalibration ... -- I'm committing because there's some kind of fundamental problem with the ReadCovariates cache, in that historical data isn't being cleared / computed properly, and I'd rather it fail for a while than leave it in JIRA. -- The integration tests test the -nct with PrintReads to get 1, 2, 4 and the 4 fails. But that's because of this incorrect calculation -- Updating GATKPerformanceOverTime with the new @ClassType annotation		2012-10-25 14:46:35 -04:00
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bqsr	Committing a broken version of BaseRecalibration	2012-10-25 14:46:35 -04:00
compression/reducereads	Refactored the BaseCounts classes so that they are safer and allow for calculations on the most probable base (which is not necessarily the most common base).	2012-10-04 10:37:11 -04:00
genotyper	MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels	2012-10-22 13:47:56 -04:00
haplotypecaller	updating HC integration test.	2012-10-24 14:08:39 -04:00