Merge branch 'master' of github.com:StructuralVariants/manta
Merge branch 'MANTA-17'

bring large-scale SV breakend assembly into master for next manta release
pre-release tweaks
update cl
fix unit test warnings
* MANTA-23

Now supports sparse BAM files (as in Variant Archive) using :-
--useExistingAlignStats
--useExistingChromDepths
update cl
forgot to revcomp one copy of the insert sequence during vcf output
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