Using Bazam to extract reads

[hdashnow]

Uses the Bazam tool (https://github.com/ssadedin/bazam) to extract relevant reads from a bam/cram file before remapping to the STR decoy genome. Because this tool pipes directly to BWA, can be run in parallel, and handles grabbing both reads in a pair correctly, this change both decreases runtime and increases sensitivity.

Also fixes errors caused by some versions of Samtools (see #25, #26)

Big thanks to @ssadedin for creating bazam!