BEGIN{
#    f="/data/results/reference/mmu/mm9/mRNA-stranded/Mus_musculus.NCBIM37.64-toMM9.headers";
    OFS="\t";
    f="/data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/myTRanno.gtf2";
    while (getline<f){
	en=$3;ne=split($4,a,"|");ein[en]=ne;
	
	for (i=2;i<=ne;i++){x=a[i];
	    ei[en,i]=substr(x,1,1);
	    split(substr(x,2),b,"-");
	    eis[en,i]=0+b[1];
	    eie[en,i]=0+b[2];
#	    print en,i,ei[en,i],eis[en,i],eie[en,i]
	}
	pcg[en]=$2;
	gi[en]=$1;
	ok[en]=1;
    }
    close(f);
    FS="\t";
}{
    en=$1;
    if (ok[en]==1){
	s=1+$2;e=$3;ncl++;iu5=0;iu3=0;icds=0;hit[en]++;
#	if (e<cdss[en]) {u5++;iu5=1;nu5[en]++;}
#	if (s>cdse[en]) {u3++;iu3=1;nu3[en]++;}
#	if ( (s>=cdss[en])&&(e<=cdse[en]) ) {cds++;icds=1;ncds[en]++;}
	ne=ein[en];x="ERR";
	for (i=2;i<=ne;i++){
	    if ((s>=eis[en,i])&&(s<=eie[en,i])){
		x=ei[en,i];break;
	    }
	}
	if (x=="ERR"){print "ERR clusterstart "s" not found, ref="en", nregions "ne" line "NR"\n"$0>>"/dev/stderr";}
#	print gi[en]"\t"pcg[en]"\t"x"\t"$0;
	print $1,$2,$3,$4,$5,gi[en]"\t"pcg[en]"\t"x;
    } else{
	print "ERR unk ENS "$0;
    }
}END{
 }