#!/bin/sh
rm -f Results
for f in *.seq
do
	base=`basename $f .seq`
	../code.d/swband1 $base.hsp $base.seq > swband.out
	../code.d/genelaps -q -e swband.out > genelaps.out
	../code.d/genedata genelaps.out > genedata.out
	../code.d/align $base.seq 2 < genedata.out > align.out 2>>Results
	../code.d/reAligner < align.out > $base.cns 2>>Results
done