We should allow options to include/exclude samples from the analysis to avoid sub-setting the VCF. I should check if the GATK framework have this implemented (at least I know that some parameters perform that). If not, the simplest way is to implement a GenotypeFilter functional interface for include/exclude genotypes, and include this in the HaplotypeWalker. Like that, all the tools will include this behaviour.
We should allow options to include/exclude samples from the analysis to avoid sub-setting the VCF. I should check if the GATK framework have this implemented (at least I know that some parameters perform that). If not, the simplest way is to implement a
GenotypeFilterfunctional interface for include/exclude genotypes, and include this in theHaplotypeWalker. Like that, all the tools will include this behaviour.