fix doxygen path
crank up the doxygen detail level
more doxygen tweaking
Update copyright text to include hoedown
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
improve manta vcf comparison utility
unit test whitespace
start subdividing SVLocusScanner
fix assembly error when filtering supp reads
update default reference to a more stable path
user guide
close clang warning
MANTA-67 add circularCounter
fluff
MANTA-67 add another edge isect filter in cand gen
MANTA-77 fix RNA-seq assertion for supp reads
MANTA-63 get pairs for small svs
update cl
MANTA-63 adjust pair search range