#bedtools multicov -bams ../bam/1A.rmdup.bam ../bam/1B.rmdup.bam ../bam/1C.rmdup.bam -bed /export/database/hg19_annotation/bed/10k_win.bed |awk 'BEGIN{print "A1" "\t" "B1" "\t" "C1"} {print $7 "\t" $8 "\t" $9}' >10k_win.test3

$rg_bed = $ARGV[0];

my @arr = qw(
tcc140
tcc136
tcc137
tcc141

);

$cmd="bedtools multicov -bams"; $awk= " |awk 'BEGIN{print \"id\" \"\\t\" "; $awk2 = "\{print \$4 \"\\t\" ";
for ($i = 0; $i <= $#arr; $i++){
$sample=$arr[$i];

$bam = $sample . ".bam";
$dep = `samtools view ../bed/bed2bam/$bam |grep chr |wc -l`;
@arr2 = split /\s/,$dep;
$dept = $arr2[0];
#$d = d."$b";
#$$d = $dept * 2;
# print"$dept\t";
$radio = 1000000/($dept);
$radio=sprintf "%0.2f",$radio;

$num=$i+7;
#print"\ts$sample";
if($i == $#arr){$awkf=$awkf . "\"$sample\"" . "\}";}
else{$awkf=$awkf . "\"$sample\"" . " \"\\t\" ";}

if($i == $#arr){$awkf2=$awkf2 . "\$$num*$radio" . "\}\'";}
else{$awkf2=$awkf2 . "\$$num*$radio" . " \"\\t\" ";}

$samplefile= "../bed/bed2bam/" . $sample . ".bam";
$cmdf = $cmdf . " $samplefile";
}
$awk = $awk . $awkf;
#print"$awk\n";

$awk2 = $awk2 . $awkf2;
#print"$awk\t$awk2\n";
$cmd = $cmd . $cmdf . " -bed $rg_bed";

print"$cmd\t$awk\t$awk2\n";