X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fbowtie2sam.pl;h=5dff88d4e96d25cba66e65cf4d3c5facaad22d21;hb=fbb4b1356096b31bb5f1956f864f4c76b21565f6;hp=4ead83991f81bab59c2a53485d2296e7b0ac6370;hpb=38c2703b74ff9a045933206123c86c4e8f999d14;p=samtools.git

diff --git a/misc/bowtie2sam.pl b/misc/bowtie2sam.pl
index 4ead839..5dff88d 100755
--- 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 = '';