Hap.py not evaluating chromosomes in regions bed

[ExpressionAnalysis]

When using the -R option to restrict the analysis to a region of interest, we noticed that variants in the query are only evaluated if they are on a chromosome with a variant in the truth. There are strong use cases for reporting all false positives in the ROI even if there are no expected variants in the truth. For example, if evaluating a small gene panel you might expect only a few variants but need to understand how many false positives are called across the ROI. Using hap.py to evaluate vcf concordance is another use case with a need for evaluating all variants regardless of the presence of variants on the chromosome.