MANTA-20 provide workflow level control of minimum sv output sizes
MANTA-20 reorganize candidate util functions
partial work of split read scoring
The first pass of scoring split read evidence
add splitReadAlignment class
fix mapQ calculation
add split read counts
add debugging info
more debugging info
fix alignment score bug
fix the bug of score thresholds
second fix of scoring thresholds
adjust evidence filter values
Merge branch 'master' into MANTA-20

Merging master into MANTA-20 after MANTA-33 was added to master

Conflicts:
	src/c++/lib/manta/SVLocusAssembler.cpp
1. add read map to avoid double counting
2. check max depth and use 2*filter_value as the cutoff to determine if split-read evidence shoule be applied.
3. a bit cleaning of the code
remove debugging info
add back debugging
debug #1
test
update cl