6309f5897de402d8b79b291054f246f9fec1bc1e
hiram
  Mon Aug 19 15:46:07 2019 -0700
correctly account for name2 index refs #24008

diff --git src/hg/utils/automation/xenoRefGeneIx.pl src/hg/utils/automation/xenoRefGeneIx.pl
index adf9bee..cdd67ee 100755
--- src/hg/utils/automation/xenoRefGeneIx.pl
+++ src/hg/utils/automation/xenoRefGeneIx.pl
@@ -88,31 +88,31 @@
 }
 
 my $gpFile = shift;
 
 if ($gpFile =~ m/.gz$/) {
   open (FH, "zcat $gpFile|") or die "ERROR: xenoRefGeneIx.pl can not read '$gpFile'";
 } else {
   open (FH, "<$gpFile") or die "ERROR: xenoRefGeneIx.pl can not read '$gpFile'";
 }
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp ($line);
   my ($chrom, $chromStart, $chromEnd, $name, $score, $strand, $thickStart, $thickEnd, $reserved, $blockCount, $blockSizes, $chromStarts, $name2, $cdsStartStat, $cdsEndStat, $exonFrames, $type, $geneName, $geneName2, $geneType) = split('\t', $line);
   my %allNames;	# key is name, value is count of times seen
   processOne(\%allNames, $name) if (length($name));
-  processOne(\%allNames, $name2) if (length($name));
+  processOne(\%allNames, $name2) if (length($name2));
   processOne(\%allNames, $geneName) if (length($geneName));
   processOne(\%allNames, $geneName2) if (length($geneName2));
   my $howMany = 0;
   foreach my $someName (keys %allNames) {
      $howMany += 1;
   }
   if ($howMany > 1) {
     printf "%s", $name;
     foreach my $someName (sort keys %allNames) {
       next if ($someName =~ m/\Q$name\E/i);
       printf "\t%s", $someName;
     }
     printf "\n";
   }
 }