Update phase change script to incorporate mate pairs

Our scripts currently just look at one read at a time, and it means that we're encountering lots of reads where there aren't enough SNPs to call phase changes. Scanning for phase changes across mate pairs will involve creating a lookup table and then using that to create tuples of bam records, from which haplotype phases can be individually determined and then combined (since phase change detection currently just boils down to looking for more than one parental phase in a read).

The ids in the qname column alongside rnext and pnext can be used to detect mate reads. See SAM specification.

ness-lab / recombinant-reads

Update phase change script to incorporate mate pairs #12