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
MANTA-20 include the last line of the vcf header
MANTA-20 more details to streamline SVEvidence
MANTA-20 add important filter to split read eval
MANTA-20 separate filters for som and dip output
MANTA-20 skip somatic score when not used
MANTA-20 minor fixes prior to master update