Mark DePristo efad215edb Greedy version of function to compute the max achievable AC for each alt allele ... -- walks over the genotypes in VC, and computes for each alt allele the maximum AC we need to consider in that alt allele dimension. Does the calculation based on the PLs in each genotype g, choosing to update the max AC for the alt alleles corresponding to that PL. Only takes the first lowest PL, if there are multiple genotype configurations with the same PL value. It takes values in the order of the alt alleles.		2012-10-15 07:53:54 -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	Greedy version of function to compute the max achievable AC for each alt allele	2012-10-15 07:53:54 -04:00
haplotypecaller	Turning on allele trimming for the haplotype caller.	2012-10-10 10:47:26 -04:00