#!/bin/bash

# adapted from erik garrion's vcfsort (in vcflib)
# https://github.com/ekg/vcflib/blob/master/bin/vcfsort
if [ ! -z "$1" ]
then
	if [ ! -z "$2" ]
	then
		awk '$0~"^#" { print $0; next } { print $0 | "sort -k1,1V -k2,2n -k3,3n -k4,4V -k5,5n -k6,6n" }' $1 >$2
	else
		awk '$0~"^#" { print $0; next } { print $0 | "sort -k1,1V -k2,2n -k3,3n -k4,4V -k5,5n -k6,6n" }' $1
	fi
else
	awk '$0~"^#" { print $0; next } { print $0 | "sort -k1,1V -k2,2n -k3,3n -k4,4V -k5,5n -k6,6n" }'
fi


