BEGIN{
    if (min>0) {mmin=min}
    q=sprintf("%c",34);
#print min" "mmin
    pa=ENVIRON["PWD"];# printf pa
    n=split(pa,a,"/");
    run= a[5];
    f="samples.txt";
    of="make-unstranded-sampled-mm9-tracks.sh";
    print "#!/bin/bash">of
    min=1e99;
    while(getline<f){	
	if (substr($1,1,3)=="Ion"){
	    rd[$2]=$5;
	    if ($5<min) {min=$5}
	}
    }
    close(f);
    if (mmin>0){
	m="# Sampling to "mmin" reads"
    } else {
	m="# Sampling to smallest library containing "min" reads"
    }
    print m	>>of
    print m

    print "">>of
    for (i in rd) {
	if (mmin>0){
	    if (rd[i]>mmin) {
		sc=1.0*mmin/rd[i];
		print "# nreads: "rd[i]
		print "/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh "i".bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome "sc
		print "/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh "i".bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome "sc>>of
	    }
	} else {
	    sc=min/rd[i];
	    print "/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh "i".bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome "sc>>of
	}
#    print "#/data/results/tools/proton/tophat2unstranded-bigwig1.sh $i /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome">>of
#    print "#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh $i /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome $sc">>of
#    print "done">>of
    }
    close(of);
    print of
    print "\nProceed? (y/n) :";
}{
    if ($1=="y") {
	m="chmod u+x "of
	system(m);
	m="./"of" &> "of".log"
	print m
	system(m);

  }
   exit;
}