open INP,"< $ARGV[0]"
        or die "Cannot open file: $!";

$file = "$ARGV[1]";

open OUT, "> $file"
        or die "Cannot open file: $!";

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 2>&1`;

print OUT @out;

close INP;
close OUT;