Before extracting the population haplotypes to generate an LD matrix, this script parses the VCF header to find the indices of the samples that belong to a certain population.
This patch decreases the time complexity of the header parsing from O(n^2) to O(n).
Before extracting the population haplotypes to generate an LD matrix, this script parses the VCF header to find the indices of the samples that belong to a certain population. This patch decreases the time complexity of the header parsing from O(n^2) to O(n).