BEGIN{
#1:Geneid
#2:Chr
#3:Start
#4:End
#5:Strand
#6:Length
#7:/data/images/proton/DKlab/run392/DKR4b-WT1M.bam
#8:DKR5_InputWt-2M.bam
#9:DKR6_InputWt-3F.bam
#10:DKR7_InputTg6105-1M.bam
#11:DKR8_InputTg6105-2M.bam
#12:DKR9-InputTg6105-3F.bam
#13:DKR13r_M2RiPWt-1M.bam
#14:DKR14r_M2RiPWt-2M.bam
#15:DKR15r_M2RiPWt-3F.bam
#16:DKR16_M2RiPTg6105-1M.bam
#17:DKR17r_M2RiPTg6105-2M.bam
#18:DKR18_M2RiPTg6105-3F.bam
#19:DKR19-HuRRiPC57-1M.bam
#20:DKR21-HuRRiPC57-3F.bam
#21:/data/images/proton/DKlab/run392/DKR20-HURRIPC57-2M.bam
#22:DKR22-IgGRiPC57-1M.bam
#23:DKR23r-IgGRiPC57-2M.bam
#24:DKR24r-IgGRiPC57-3F.bam
#25:DKR10-InputC57-1M.bam
#26:DKR11-InputC57-2M.bam
#27:DKR12-InputC57-3F.bam
    for (i=1;i<7;i++){os[i]=1;}
    for (i=13;i<25;i++){os[i]=1;}
    f="/data/images/proton/DKlab/run392/run402/featurecount-log.txt";
    while (getline<f){
	tr[$1]=$2;
#	print $1,$2;
    }
    close(f)
    FS=OFS="\t";
    getline;
    getline;
#    print $0;
    ns=NF;
    printf("%s",$1);
    for (i=2;i<=ns;i++){
#	print i":"$i;
	if (os[i]){printf("\t%s",$i);}
    }
    printf("\tiWT\tiTg6105\tiC57\n");
    for (i=7;i<=ns;i++){
	n=split($i,a,"/");
	sampID[i]=substr(a[n],1,length(a[n])-4);
#	print sampID[i],tr[sampID[i]]	
	tr2[i]=tr[sampID[i]];
	if (tr2[i]==0) {print "ERR : "sampID[i]" not found in "f}
    }
}{
	fl[NR]=$6;ns=NF;
	for (i=1;i<7;i++){
	    r[NR,i]=$i;
	}
	for (i=7;i<=ns;i++){
	    x=$i;
	    nr[i]+=x;
	    r[NR,i]=x;
	}
} END {
	nl=NR;
#    print "Sample","Total_mapped_reads"
#    ofn1[ctl1i]="RPKM_"ctl1"_vs_"ctl2;
    for (i=7;i<=ns;i++){
	rpm[i]=tr2[i]/1000000.0;
#	print sampID[i],nr[i] >>"
    }
    for (l=3;l<=nl;l++){
	printf("%s",r[l,1]);
	for (i=2;i<7;i++){
	    printf("\t%s",r[l,i]);
	}
	kb=fl[l]*0.001;
#	print r[l,1],kb
        for (i=7;i<=ns;i++){
	    rpkm[l,i]=(r[l,i]/rpm[i])/kb;
	}
	iWT=(rpkm[l,7]+rpkm[l,8]+rpkm[l,9])/3.0;
	iTg=(rpkm[l,10]+rpkm[l,11]+rpkm[l,12])/3.0;
	iC57=(rpkm[l,25]+rpkm[l,26]+rpkm[l,27])/3.0;	
	for (i=7;i<=ns;i++){
	    if (os[i]){
		if (rpkm[l,i]==0){
		    printf("\t0");
		} else {
		    printf("\t%f",rpkm[l,i]);
		}
	    }
	}
#	printf("\t%f\t%f\t%f; %f,%f,%f\n",iWT,iTg,iC57, rpkm[l,7],rpkm[l,8],rpkm[l,9]);
	printf("\t%f\t%f\t%f\n",iWT,iTg,iC57);	
    }
 }