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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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	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	Ready for full-scale evaluation adaptive BQSR contexts	2012-08-03 16:02:53 -04:00