c300fe6d73053e74556dcdff06ee7abbfda8268a
hiram
  Wed Aug 20 09:13:29 2025 -0700
alternate alias name list up to date refs #34337

diff --git src/hg/utils/automation/aliasTextToBed.pl src/hg/utils/automation/aliasTextToBed.pl
index 7728a028efd..59b3421be8d 100755
--- src/hg/utils/automation/aliasTextToBed.pl
+++ src/hg/utils/automation/aliasTextToBed.pl
@@ -57,54 +57,60 @@
 open (SZ, "<$opt_chromSizes") or die "can not read the chromSizes: $opt_chromSizes\n";
 while (my $line = <SZ>) {
   chomp $line;
   my ($chrom, $size) = split('\s+', $line);
   $chromSizes{$chrom} = $size;
 }
 close (SZ);
 
 my %nameLabels = (
    "assembly" => "Assembly",
    "genbank" => "GenBank",
    "ncbi" => "NCBI",
    "refseq" => "RefSeq",
    "ucsc" => "UCSC",
    "ensembl" => "Ensembl",
+   "xenbase" => "Xenbase",
+   "chrNames" => "chrNames",
+   "chrN" => "chrN",
+   "VEuPathDB" => "VEuPathDB",
    "custom" => "custom"
 );
 
 open (AS, ">$opt_aliasAs") or die "can not write to $opt_aliasAs";
 
 my $indexNames;
 
 $titleLine =~ s/^#\s+//;
 my @legendNames = split('\s+', $titleLine);
 my $expectFieldCount = scalar(@legendNames);
 my $i = 0;
 # output the .as definition
 printf AS "table chromAlias\n";
 printf AS "   \"chromAlias bigBed index\"\n";
 printf AS "    (\n";
 printf AS "    string chrom;\t\"native sequence name\"\n";
 printf AS "    uint chromStart;\t\"always 0\"\n";
 printf AS "    uint chromEnd;\t\"chromosome size\"\n";
 foreach my $title (@legendNames) {
   if (length($indexNames)) {
     $indexNames .= "," . $title;
   } else {
     $indexNames = $title;
   }
+  die "not defined title" if (!defined($title));
+  die "not defined nameLabels{$title}" if (!defined($nameLabels{$title}));
   printf AS "    string %s;\t\"%s name\"\n", $title, $nameLabels{$title};
 }
 printf AS "    )\n";
 close (AS);
 
 printf STDERR "# indexNames: '%s'\n", $indexNames;
 
 open (BD, "|sort -k1,1 -k2,2n>$opt_aliasBed") or die "can not write to $opt_aliasBed";
 
 while (my $line = <FH>) {
   chomp $line;
   my @a = split('\t', $line, -1); # the -1 keeps all empty fields too
   if (scalar(@a) != $expectFieldCount) {
      printf STDERR "ERROR: expected field count %d =! %d on line %d\n", $expectFieldCount, scalar(@a), $.;
      exit 255;