count-af.nim

import hts/vcf
import os

var gnomad_path = commandLineParams()[0]

var
  gvcf:VCF
  total:int
  mid:int

if not open(gvcf, gnomad_path, threads=3):
  quit "could not open vcf"

var af = newSeq[float32](1)
for v in gvcf:
  if v.info.get("AF", af) != Status.OK: continue
  total += 1
  if af[0] > 0.05: mid += 1

echo "> 0.05:", mid
echo "count:", total
echo "pct:", 100'f64 * (mid / total)