calc_qall ***********************************************************
calc_qall(Pvalue_threshold, fracInvalid_threshold, fracNA_threshold, Pvalue,
fracInvalid, F1.NAfrac, matchParents, bestfit, bestParentfit, par.conflicts,
par.NAfrac, critweight, parentsScoredWithF1)Threshold can be disabled by setting to 0
Threshold can be disabled by setting to 1
Threshold can be disabled by setting to 1
P-value of bestParentfit segtype
Fraction invalid scores of the bestParentfit segtype
fraction missing scores among F1 samples
Should parents match F1? One of the following: "No", "Unknown", "OneOK" or "Yes"
segtype of best fit of population
segtype of best fit of parents
Logical vector: is there a conflict for P1, P2
number of NA scores for the samples of P1, P2
numeric vector of length 3 (3 quality criteria) with their weights, or NA (in that case qall = q1*q2*q3, not a weighted average)
Were parents scored with F1?
vector of length 4 or 5. The last (two) components of the vector are qall_mult (obtained by multiplication of q1..q3), and if critweights is supplied, qall_weights (a weighted average of q1..q3)