98a8fb9dfe585027839a944b73cb84f0a244f0ae
hiram
  Sat Sep 24 18:36:17 2022 -0700
adding custom category to handle TOGA name changes refs #29982

diff --git src/hg/utils/automation/aliasTextToBed.pl src/hg/utils/automation/aliasTextToBed.pl
index fa24d44..ba33a60 100755
--- src/hg/utils/automation/aliasTextToBed.pl
+++ src/hg/utils/automation/aliasTextToBed.pl
@@ -56,31 +56,32 @@
 my %chromSizes;	# key is chrom name, value is size
 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"
+   "ensembl" => "Ensembl",
+   "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";