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
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downsampling	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
walkers	Bugfix for GSA-647 HaplotypeCaller misses good variant because the active region doesn't trigger for an exome	2012-11-01 15:34:04 -04:00