5d19fca649
1) SelectVariants could throw a ReviewedStingException (one of the nasty "Bug:") ones if the user requested a sample that wasn't present in the VCF. The walker now
checks for this in the initialize() phase, and throws a more informative error if the situation is detected. If the user simply wants to subset the VCF to
all the samples requested that are actually present in the VCF, the --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES flag changes this UserException to a Warning,
and does the appropriate subsetting. Added integration tests for this.
2) GenotypeLikelihoods has an unsafe method getLog10GQ(GenotypeType), which is completely broken for multi-allelic sites. I marked that method
as deprecated, and added methods that use the context of the allele ordering (either directly specified or as a VC) to retrieve the appropriate GQ, and
added a unit test to cover this case. VariantsToBinaryPed needs to dynamically calculate the GQ field sometimes (because I have some VCFs with PLs but no GQ).
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