Guillermo del Angel 238d55cb61 Fixes for running HaplotypeCaller with reduced reads: a) minor refactoring, pulled out code to compute mean representative count to ReadUtils, b) Don't use min representative count over kmer when constructing de Bruijn graph - this creates many paths with multiplicity=1 and makes us lose a lot of SNP's at edge of capture targets. Use mean instead		2012-08-06 20:22:12 -04:00
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src/org/broadinstitute/sting	Fixes for running HaplotypeCaller with reduced reads: a) minor refactoring, pulled out code to compute mean representative count to ReadUtils, b) Don't use min representative count over kmer when constructing de Bruijn graph - this creates many paths with multiplicity=1 and makes us lose a lot of SNP's at edge of capture targets. Use mean instead	2012-08-06 20:22:12 -04:00
test/org/broadinstitute/sting/gatk/walkers	Fixed 2 haplotype caller unit tests: a) new interface for addReadLikelihoods() including read counts, b) disable test that test basic DeBruijn graph assembly, not ready yet	2012-08-03 14:26:51 -04:00