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
merge master into MANTA-20
MANTA-20 a simplistic reference allele pair support counter
MANTA-20 fix inverted assertion
MANTA-20 fix issue with fragment length estimation
fix off-by-one issue with HOMLEN and HOMSEQ
attempt to improve detection of small non-assembling indels
build tweaks
format cppcheck warnings so that IDEs can locate them
MANTA-20 initial changes to output a germline vcf
format refresh
MANTA-20 fixes to get temp diploid output
MANTA-20 fix FORMAT/SAMPLE output
MANTA-20 Gather all fragment evidence in 1 object