03456e3b8643743836b3c76c667ddd8ed6d4af82
hiram
  Thu Nov 26 22:26:55 2020 -0800
fixup chromAlias build for NCBI named assemblies and have duplicates refs #24396

diff --git src/hg/utils/automation/asmHubChromAlias.pl src/hg/utils/automation/asmHubChromAlias.pl
index 31409c1..f2c6de9 100755
--- src/hg/utils/automation/asmHubChromAlias.pl
+++ src/hg/utils/automation/asmHubChromAlias.pl
@@ -99,32 +99,32 @@
 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+', $line);
 ### early version    my ($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});
+    } elsif (defined($ncbiToUcsc{$dupTarget})) {
+        addAlias($dupAlias, $ncbiToUcsc{$dupTarget});
     } else {
       printf STDERR "# ERROR: can not find duplicate name $dupAlias for sequence $dupTarget\n";
       $dupsNotFound += 1;
     }
     ++$dupCount;
   }
   close (FH);
 }
 
 if ($dupsNotFound > 0) {
   printf STDERR "ERROR: can not find %d duplicate names\n", $dupsNotFound;
   exit 255;
 }
 
 if ($sequenceCount != $nameCount) {