fix a bug in split read scoring
add back debugging mode
add SVAlignInfo for debugging
Reverting last commit, was supposed to go into branch, sorry
extend somatic contigs
Close warnings from clang scan-build
fix off-by-one index error in small-assembler test
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
add a check in split read alignment to deal with the corner case where the breakpoint is located at the first base of reference sequence.
Adding timing info to debug out in candidate generation
Merge branch 'master' of github.com:StructuralVariants/manta
Fixing cppcheck 1.58 warning
Add verbose switch to GenerateSVCandidates

This switch enables relatively lightweight, high-level
logging to assists with debug triage
Include the chromosome key in verbose output
MANTA-39 prevent crash on large CIGAR deletions
tweak verbose output
fix verbose output when DEBUG_GSV is defined
add new assertions based on split-read debug case
include read key types from Grouper