This commit makes some radical changes to the dng-call internals.
dng-call can now estimate variants and report them if the --all flag is added to the command line.
The quality field of the vcf is now set and contains the quality that the site contains a founding variant or a denovo mutation. It is calculated as -10.0*log10(P(site is monomorphic ref))
Additional flags are used in the INFO field to report if a site contains a putative and whether that de novo may be a germline, somatic, or library variant.
Additional information is recorded in the ##PEDIGREE lines, including ploidy
The genotype prior is now a proper finite-sites model again.
The mutation model as been reengineered to calculate P(1 mutation) and Expected number exactly.
dng-call now skips a site early if it can
MUTQ now reports the quality of a de novo mutations
This commit makes some radical changes to the dng-call internals.
--allflag is added to the command line.-10.0*log10(P(site is monomorphic ref))##PEDIGREElines, including ploidy