* MANTA-30

If EstimateSVLoci is provided with an option truth VCF file, it outputs
information about SVObservation detections of variants in that truth set.
Sync to 2013_11_19 master

Conflicts:
	src/c++/lib/applications/EstimateSVLoci/EstimateSVLoci.cpp
	src/c++/lib/applications/EstimateSVLoci/SVLocusSetFinder.cpp
	src/c++/lib/applications/EstimateSVLoci/SVLocusSetFinder.hh
	src/c++/lib/applications/GenerateSVCandidates/SVFinder.cpp
	src/c++/lib/applications/GenerateSVCandidates/SVFinder.hh
	src/c++/lib/manta/SVLocusScanner.cpp
	src/c++/lib/manta/SVLocusScanner.hh
	src/c++/lib/manta/test/SVLocusScannerTest.cpp
* MANTA-30

Merge fixes.