baq: Fix scanning for start of read window in cap_baq_qualities
baq: Fix scanning for start of read window in cap_baq_qualities

If the clipped part of the read includes indels, cap_baq_qualities
would erroneously mark the first indel as the start for the read window.

Check for invalid read coordinates while scanning for the read window
start.

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