Further optimize DP, VAF, and strand bias calculation

[gtollefson]

DP, VAF, and strand bias calculation takes a very long time because each indel range is used to query the bam file using readGAlignments() to retrieve information needed to calculate indel position coverage and distribution of +/- strands in reads at the indel position.

This could be made less expensive by querying the bam file only once using a Granges object of all indel ranges and then performing vectorized operations in parallel on the returned GAlignment object.