Mark DePristo ec935f76f6 Initial implementation and tests for IndependentAllelesDiploidExactAFCalc ... -- This model separates each of N alt alleles, combines the genotype likelihoods into the X/X, X/N_i, and N_i/N_i biallelic case, and runs the exact model on each independently to handle the multi-allelic case. This is very fast, scaling at O(n.alt.alleles x n.samples) -- Many outstanding TODOs in order to truly pass unit tests -- Added proper unit tests for the pNonRef calculation, which all of the models pass		2012-10-15 07:53:55 -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	Initial implementation and tests for IndependentAllelesDiploidExactAFCalc	2012-10-15 07:53:55 -04:00
haplotypecaller	Turning on allele trimming for the haplotype caller.	2012-10-10 10:47:26 -04:00