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
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
Correct SVAlignInfo to extract the spanning alignment only when the sv is spanning
Merge remote-tracking branch 'origin/MANTA-20'
update cl