Mark DePristo eaffb814d3 IndependentExactAFCalc is now the default EXACT model implementation ... -- Changed UG / HC to use this one via the StandardCallerArgumentCollection -- Update the AFCalcFactory.Calculation to have a getDefault() value instead of having a duplicate entry in the enums		2012-10-21 12:42:31 -04:00
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bqsr	updating BQSR integration tests	2012-09-19 14:10:34 -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	IndependentExactAFCalc is now the default EXACT model implementation	2012-10-21 12:42:31 -04:00
haplotypecaller	Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.	2012-10-20 16:38:18 -04:00