Menachem Fromer 6984ab0c78 Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing		2013-01-08 16:40:32 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing	2013-01-08 16:40:32 -05:00
test	Fixed precision problem in the Bayesian calculation of Qemp: we need to cap below max integer because the MathUtils code add +1.	2013-01-07 13:07:36 -05:00