Compute (uncorrected) 1-Q1 for each block-jackknife block (if any) and over all the SNPs (i.e., either within or outside blocks)
.compute_H1(refcount, totcount, nblocks, block_id, verbose)Return a matrix with npops rows and nblocks+1 column giving the mean H1 of each pop within each block and for all SNPs (last column)
Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele
Matrix of nsnpxnpop with total counts or read coverages
Integer giving the number of block-jackknife blocs (may be 0 if no block-jackknife)
Integer vector of length nsnps with the (0-indexed) id of the block to which each SNP belongs (-1 for SNPs outside blocks)
Logical (if TRUE progression bar is printed on the terminal)
Compute all the (uncorrected) H1=1-Q1 for each block-jackknife block (if any) and overall SNPs (within or outside blocks). It is indeed more convenient to compute H1 (rather than Q1) to apply corrections afterwards within R function