clarify docs
MANTA-118 static libstdc++

when gcc 4.5+ is used, libstdc++ and libgcc will be
statically linked to improve portability
update cl
MANTA-116 fix region mode for 2 close regions

previous error was caused by a duplicated task label during graph build
add SA to bam debug output
MANTA-116 adjust orientation of SA split candidates
update cl
fix cppcheck issue
don't disable sv scoring when depth filter is off
fix typo
Adding split-read MAPQ=0 filtering: "if (atoi(saDat[4].c_str()) == 0) return;" This can be changed later to be set to 20 as is done for pair MAPQ values.
Merge branch 'master' of https://github.com/StructuralVariants/manta
refine SA MAPQ filtration details
Merge branch 'master' into MANTA-78
Fix to debug out in SVScoreInfoDiploid
Merge branch 'master' of github.com:StructuralVariants/manta
Merge branch 'master' into MANTA-78