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
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Added more options to control RBP behavior; raised default RBP PQ threshold to 20
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Have all significant XHMM commands be run with LongRunTime
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Use GenomeLocParse in a non-deprecated way
Fix to only consider the samples that are both in the PED file and in the VCF file
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Fix to deal with multi-generational families being allowed if only one level (one 'trio', effectively) appears in the VCF
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Fixed a few typos and clarified some doc points.
Merge pull request #385 from broadinstitute/gg_vqsr_docfixes

Fixed a few typos and clarified some doc points.
Merged bug fix from Stable into Unstable