#!/usr/bin/env bash
if [[ $# != 3 ]] ; then
    echo "Usage:"
    echo "$0 in.exon.gtf in.bed intersect_out.bed"
    exit
fi

exon_gtf=$1
in_bed=$2
out_bed=$3

tmp=${out_bed}.tmp.out

# 0. intersect exon.gtf and in_bed
#>&2 echo "bedtools intersect -s -a ${exon_gtf} -b ${in_bed} -split > $tmp"
bedtools intersect -s -a ${exon_gtf} -b ${in_bed} -split > $tmp

# 2. gtf => bed
#>&2 echo "gtf2bed $tmp $out_bed"
gtf2bed $tmp $out_bed
rm $tmp
