Guillermo del Angel c9a4c74f7a a) Bug fixes for last commit related to PileupElements (unit tests are forthcoming). b) Changes needed to make pool caller work in GENOTYPE_GIVEN_ALLELES mode c) Bug fix (yet again) for UG when GENOTYPE_GIVEN_ALLELES and EMIT_ALL_SITES are on, when there's no coverage at site and when input vcf has genotypes: output vcf would still inherit genotypes from input vcf. Now, we just build vc from scratch instead of initializing from input vc. We just take location and alleles from vc		2012-02-24 10:27:59 -05:00
..
config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	a) Bug fixes for last commit related to PileupElements (unit tests are forthcoming). b) Changes needed to make pool caller work in GENOTYPE_GIVEN_ALLELES mode c) Bug fix (yet again) for UG when GENOTYPE_GIVEN_ALLELES and EMIT_ALL_SITES are on, when there's no coverage at site and when input vcf has genotypes: output vcf would still inherit genotypes from input vcf. Now, we just build vc from scratch instead of initializing from input vc. We just take location and alleles from vc	2012-02-24 10:27:59 -05:00
test	int <-> BitSet conversion utils for MathUtils	2012-02-21 14:10:36 -05:00