Fix missing declaration for getopt on Mac OS X

[samtools.git] / misc / bowtie2sam.pl

diff --git a/misc/bowtie2sam.pl b/misc/bowtie2sam.pl
index 4ead83991f81bab59c2a53485d2296e7b0ac6370..5dff88d4e96d25cba66e65cf4d3c5facaad22d21 100755 (executable)
--- a/misc/bowtie2sam.pl
+++ b/misc/bowtie2sam.pl
@@ -12,7 +12,7 @@ exit;
 
 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 = '';