MANTA-17 add semi-aligned reads to discovery/score

Note this is the contents of the MANTA-17-fixed branch
flattened to one commit and reformatted.
MANTA-17 use semi-aligned reads in discovery/score

This contains integration changes applied to the original
MANTA-17-fixed branch prior to merging. The primary change
is to reduce the contents to include only the semi-aligned
read feature for the purpose of merging/testing one feature
at a time