#! /bin/bash
gnom=_GENOME_

tags=_TAGS_
pks=_PKS_
dens=_DENS_

bin=_BINDIR_RAPPH_
fdrs=_FDRS_
K=_K_

name=`basename $tags`
denb=`basename $dens`
if [ ! -e $denb ]; then
    ln -s $dens $denb
fi
for fdr in $fdrs
do
    wig=$name-both-passes/$name.hotspot.twopass.fdr$fdr.merge.wig
    tout=$name-both-passes/$name.hotspot.twopass.fdr$fdr.merge.pks.tmp.bed
    combbed=$name-both-passes/$name.hotspot.twopass.fdr$fdr.merge.pks.bed
    combwig=`echo $combbed | sed s/bed$/wig/`
    echo $combwig
    setops -e -0% $pks $wig > $tout
    trname=$name.pks.fdr$fdr
    $bin $wig $denb.jarch $tout $combbed
    echo "track name=$trname" > $combwig
    cut -f1-3 $combbed >> $combwig
    rm $tout
done
