b1852a4dd2bbc53c29c822f0d6a0e40d1af7a713
hiram
  Wed Sep 23 10:11:32 2020 -0700
accomodate duplicate sequences refs #24396

diff --git src/hg/utils/automation/asmHubChromAlias.pl src/hg/utils/automation/asmHubChromAlias.pl
index c8bfe1c..68a5561 100755
--- src/hg/utils/automation/asmHubChromAlias.pl
+++ src/hg/utils/automation/asmHubChromAlias.pl
@@ -91,32 +91,32 @@
   $ucscNames = 1 if (defined($sequenceSizes{$ucscName}));
   if ($refSeq) {
     $ucscToRefSeq{$ucscName} = $seqName;
   } else {
     $ucscToGenbank{$ucscName} = $seqName;
   }
 }
 close (FH);
 
 my $dupsNotFound = 0;
 my $dupsList = "../../download/$asmId.dups.txt.gz";
 if ( -s "$dupsList" ) {
   open (FH, "zcat $dupsList | awk '{print \$1, \$3}'|") or die "can not read $dupsList";
   while (my $line = <FH>) {
     chomp $line;
-#    my ($dupAlias, $dupTarget) = split('\s+', $line);
-    my ($dupTarget, $dupAlias) = split('\s+', $line);
+    my ($dupAlias, $dupTarget) = split('\s+', $line);
+### early version    my ($dupTarget, $dupAlias) = split('\s+', $line);
     if ($ucscNames) {
       if (!defined($ncbiToUcsc{$dupTarget})) {
        printf STDERR "# ERROR: can not find dupTarget: $dupTarget in ncbiToUcsc for dupAlias: $dupAlias\n";
          $dupsNotFound += 1;
       } else {
         addAlias($dupAlias, $ncbiToUcsc{$dupTarget});
       }
     } elsif (defined($ucscToNcbi{$dupTarget})) {
         addAlias($dupAlias, $ucscToNcbi{$dupTarget});
     } else {
       printf STDERR "# ERROR: can not find duplicate name $dupAlias for sequence $dupTarget\n";
       $dupsNotFound += 1;
     }
     ++$dupCount;
   }