sub bowtie2sam {
my %opts = ();
- die("Usage: bowtie2sam.pl <aln.bowtie>\n") if (@ARGV == 0);
+ die("Usage: bowtie2sam.pl <aln.bowtie>\n") if (@ARGV == 0 && -t STDIN);
# core loop
my (@s, $last, @staging, $k, $best_s, $subbest_s, $best_k);
$last = '';