#!/usr/bin/env bash
if [[ $# != 2 ]] ; then
    echo "Usage:"
    echo "$0 in.bed out.exon.gtf"
    exit
fi

in_bed=$1
exon_gtf=$2
tmp_gtf=${exon_gtf}.tmp.gtf

# 0. bed => gtf
#>&2 echo "bed2gtf ${in_bed} $tmp_gtf isocirc"
bed2gtf ${in_bed} $tmp_gtf isocirc

# 1. gtf => exon.gtf
#>&2 echo "awk '(\$3==\"exon\"){print}' $tmp_gtf > ${exon_gtf}"
awk '($3=="exon"){print}' $tmp_gtf > ${exon_gtf}
rm $tmp_gtf
