#!/usr/bin/env bash

help_info="merge two coding file to pair file"
Usage="./mk_pair.sh dir1 dir2 outdir"
indir1=$1
indir2=$2
outdir=$3

mkdir ${outdir}
for i in ${indir1}/*
do
    filename=${i##*/}
    basename=${filename%.*}
    outfile=${outdir}/${basename}.pair
    j="${indir2}/${filename}"
    if [[ ! -f ${j} ]];then
        echo "no pair"
        exit 1
    fi
    awk 'FNR==1 && NR!=1{next;}{print}' ${i} ${j} > ${outfile}
done