MANTA-17 possible implementation for getSemiAlignedMetric
MANTA-17 switching debug messages off, slow-down not tolerable
MANTA-17 Including reads which are either semi-aligned or clipped
MANTA-17 resync with master
Merge branch 'master' into MANTA-17
MANTA-17 Fixing small variant assembly routine
MANTA-17 Reverting semi-aligned read check
MANTA-17 re-sync with master, pulling small SV changes
Merge branch 'master' into MANTA-17
MANTA-17 some post-merging fixes
MANTA-17 Adding verbose debug out
MANTA-17 Adding mapq check to shadow read test
MANTA-17 checking for mapq of singleton during shadow read test
MANTA-17 Prototype implementation of shadow reads for graph construction
MANTA-17 fix to shadow read detection
MANTA-17 Extending ref context during alignment
MANTA-17 bugfix for graph generation from shadow reads
MANTA-17 Adding unit tests for semi-aligned reads
MANTA-17 Adding shadow reads to locus graph
MANTA-17 Adding avg quality score filter for shadow reads