Eric Banks b07106b3a7 Reimplement the allele biased downsampling to be smarter. Now we don't blindly pull n% of reads off of each allele. Instead, we try all possible genotype conformations for the contaminating sample and choose the one that provides the best genotype for the target sample (based heuristically on allele balance). This method allows us to save some of the reads that belong to the target sample, which should make Daniel M happy. Added unit tests to test the biased downsampling functionality.		2012-11-06 14:39:58 -08:00
..
gatk	Reimplement the allele biased downsampling to be smarter. Now we don't blindly pull n% of reads off of each allele. Instead, we try all possible genotype conformations for the contaminating sample and choose the one that provides the best genotype for the target sample (based heuristically on allele balance). This method allows us to save some of the reads that belong to the target sample, which should make Daniel M happy. Added unit tests to test the biased downsampling functionality.	2012-11-06 14:39:58 -08:00
utils/pairhmm	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