BEGIN{
    FS=OFS="\t";
#    f="/data/images/proton/DKlab/orsalia/stringtie/comare1.annotated.gtf";
    if (length(f)==0){
    f="/data/images/proton/DKlab/orsalia/stringtie/merged.gtf";
    }
    print "read ref transcripts from "f >>"/dev/stderr"
    getline<f;h="id "$0;
    print "ref transcripts header"h >>"/dev/stderr"
    while(getline<f){nr++;
	if ($3=="transcript"){x=$9;#nr++;
	    n=split(x,a,";");
	    tid=substr(a[2],16);
	    gid=substr(a[1],9);
#	    if (nr==126826){		print tid" "gid" "x}
	    if (ok[tid]==1){print "DUP"$0}
	    tgid[tid]=gid;ok[tid]=1;
	    if (substr(a[3],2,9)=="gene_name"){tgidn[tid]=substr(a[3],12);}else{tgidn[tid]="NA";}
	}
    }
    close(f);
    print "ref transcripts "nr >>"/dev/stderr"
    FS=OFS=" ";
}{
    f1=$1; f=substr(f1,1,length(f1)-4);
    of=f".withGID.csv";
    he[f]=1;
    getline<f1;n=0;
    print "geneName geneID transcriptID "$0>of;
    while(getline<f1){
	id=$1;n++;
	if (ok[id]==1){print tgidn[id]" "tgid[id]" "$0>>of;}else{print "UNK "$0;}
    }
    close(f1);
    close(of);    
    print "transcripts in "f" to "of" : "n >>"/dev/stderr"
}