fix a bug in split read scoring
add back debugging mode
add SVAlignInfo for debugging
extend somatic contigs
prepare to merge into master
Merge branch 'MANTA-20-xchen'
1) padding somatic contigs with reference regions
2) make refSeqs in SVCandidateAssemblyData to be forward strand all the time
3) fixed a few bugs in split-read scoring

Conflicts:
	src/c++/lib/manta/SVLocusAssembler.cpp
	src/c++/lib/manta/SVLocusScanner.cpp
	src/c++/lib/manta/SVLocusScanner.hh