MANTA-17 use hypothetical breakend direction to filter the split read scan
MANTA-17 Rewriting semi-aligned test to use apath
MANTA-17 Fix assembly for inv HCC1187 chr12:33864380
Merge branch 'master' into MANTA-17

Conflicts:
	src/c++/lib/applications/GenerateSVCandidates/SVCandidateAssemblyRefiner.cpp

Update master to MANTA-17 so that we can put the chr12 inv assembly fix back onto master
MANTA-17 gcc compiler error
update cl