I had a user write to me who pointed out that the number of SNPs reported in the HTML file don't match up with the VCF. This is because I originally interpreted the first line of the vcftools summary file to report all discovered SNPs (in raw vcf), when it is actually the number of SNPs that pass the filter flags. This PR updates the tabulation so the HTML correctly reports the total number of SNPs discovered, the number filtered, and the correct theta.
I had a user write to me who pointed out that the number of SNPs reported in the HTML file don't match up with the VCF. This is because I originally interpreted the first line of the vcftools summary file to report all discovered SNPs (in raw vcf), when it is actually the number of SNPs that pass the filter flags. This PR updates the tabulation so the HTML correctly reports the total number of SNPs discovered, the number filtered, and the correct theta.