b4924336d330068ac4c39222f6cd730d33f486a1
hiram
  Thu Mar 6 15:35:53 2025 -0800
can also fixup geneName2 when transition takes place refs #32704

diff --git src/hg/utils/automation/updateName2.pl src/hg/utils/automation/updateName2.pl
index bc0a8188702..aa4d9cb3cf2 100755
--- src/hg/utils/automation/updateName2.pl
+++ src/hg/utils/automation/updateName2.pl
@@ -43,35 +43,39 @@
          }
          last;
      }
   }
 }
 close ($fh);
 
 my $updatedNames = 0;
 my $totalItems = 0;
 open ($fh, "-|", "genePredToBigGenePred $gpFile stdout") or die "can not read $gpFile";
 while (my $line = <$fh>) {
   chomp $line;
   ++$totalItems;
   # the -1 keeps the trailing empty field at the end of the line
   my @a = split(/\t/, $line, -1);
-  # if name is equal to name2 see if name2 can be improved
+  # if name is equal to geneName see if geneName can be improved
   if ($a[3] eq $a[17]) {
      if (defined($geneId{$a[3]})) {
         $a[17] = $geneId{$a[3]};
         ++$updatedNames;
+        # if name2 is equal to geneName2 reproduce name in geneName2
+        if ($a[12] eq $a[18]) {
+             $a[18] = $a[3];
+        }
      }
   }
   printf "%s\n", join("\t", @a);
 }
 close ($fh);
 printf STDERR "### updated %d items of total %d - %s\n", $updatedNames, $totalItems, $gpFile;
 
 __END__
 
 00      NW_027257890.1
 01      99779
 02      105382
 03      XM_071090490.1
 04      0
 05      +