baq: Adjust for read clipping when computing HMM reference window
baq: Adjust for read clipping when computing HMM reference window

GATK hard-clips sequencing adapters and soft-clip regions, leaving hard
clips in the CIGAR operator. The logic that detects leading/trailing
insertions checks if the first/last CIGAR operator is I, which means
that clipped reads never have lead/trail insertion regions.

Detect read clipping when computing the HMM reference window. Adjust
for leading/trailing insertions only if the read was clipped at the
corresponding end.

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