4a1540ff08c68fd435e71eeefe579e368ad8211a
angie
  Wed Dec 14 14:51:15 2016 -0800
Doh, an early extra close() on a filehandle... refs #12216 note-27

diff --git src/hg/utils/vai.pl src/hg/utils/vai.pl
index cc83e85..d6fef54 100755
--- src/hg/utils/vai.pl
+++ src/hg/utils/vai.pl
@@ -171,31 +171,30 @@
   # If input begins with # header lines, collect those into a header string.
   # Once we get to the first line of data, see if it looks like rsIds.
   # If it does, set rsId input parameters.  If not, complain and abort.
  # or none of the above (in which case, complain and abort).
   my ($inputFile) = @_;
   my $header;
   my $type;
   open(my $inFh, $inputFile) || die "Can't open inputFile '$inputFile': $!\n";
   my $firstLine = <$inFh>;
   chomp $firstLine; chomp $firstLine;
   while (defined $firstLine && ($firstLine =~ /^\s*#/ || $firstLine =~ /^\s*$/)) {
     $header .= "$firstLine\n";
     $firstLine = <$inFh>;
     chomp $firstLine; chomp $firstLine;
   }
-  close($inFh);
   if (looksLikeRsIds($firstLine)) {
     $hgVaiParams{hgva_variantIds} = rsIdStringFromInput($inFh, $firstLine);
     $hgVaiParams{hgva_variantTrack} = 'hgva_useVariantIds';
   } else {
     print STDERR "Unrecognized input format: please provide input file(s) formatted as\n" .
       "VCF, pgSnp or text with one dbSnp rsNNNN ID per line.\n";
     usage(-1);
   }
   close($inFh);
 } # autodetectRsId
 
 
 sub runHgVai(@) {
   my ($command) = @_;
   my $origDir = getcwd;