#!/bin/bash
python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/clusterize.py -f gff -i $1 -o intermedia.gff3 -c -d 150
awk '{if ($3!="exon") {print $0}}' intermedia.gff3 > intermedia.gff
#perl sortGff.pl -i intermedia.gff > $2
python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/CollapseReads.py -i intermedia.gff -f gff -o $2
