3 Commits (ddcb33fcf81cd208bc8ad6e23aeb1eb49624ea07)

Author	SHA1	Message	Date
Mauricio Carneiro	2a4ccfe6fd	Updated all JAVA file licenses accordingly ... GSATDG-5	2013-01-10 17:06:41 -05:00
Eric Banks	0a2dded093	Fixes for bugs uncovered by unit tests	2012-11-06 16:07:40 -08:00
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