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
MANTA-20 reduce qname collision detection stringency
build tweaks
format cppcheck warnings so that IDEs can locate them
MANTA-20 initial changes to output a germline vcf
format refresh