snp_filter: Simplify read bp filter
snp_filter: Simplify read bp filter

Instead of attempting to calculate the start and end locations of each
feature in the read, traverse the reference and read index lists to
find the correct positions.

This simplifies the code and fixes a number of latent bugs with minimal
performance impact.

broadinstitute/firepony,broadinstitute/firepony,NVlabs/firepony,NVlabs/firepony,NVlabs/firepony,broadinstitute/firepony,NVlabs/firepony,broadinstitute/firepony