be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/utils/automation/parseLrgXml.pl src/hg/utils/automation/parseLrgXml.pl
index bb28d0f..7052075 100755
--- src/hg/utils/automation/parseLrgXml.pl
+++ src/hg/utils/automation/parseLrgXml.pl
@@ -126,31 +126,31 @@
   $lrgSource =~ s/^\s*(.*?)\s*$/$1/;
   $lrgSourceUrl =~ s/^\s*(.*?)\s*$/$1/;
   # watch out for URLs that are just hostnames (no protocol)
   if ($lrgSourceUrl !~ /^\w+:\/\//) {
     $lrgSourceUrl = "http://" . $lrgSourceUrl;
   }
   my $creationDate = $dom->findvalue('/lrg/fixed_annotation/creation_date');
 
   foreach my $refMapping (@refMappings) {
     # Find BED 12+ fields.
     my $mapType = $refMapping->findvalue('@type');
     my $seq = $refMapping->findvalue('@other_name');
     if ($seq eq 'unlocalized') {
       $seq = "Un";
     }
-    if ($mapType eq 'haplotype' || $mapType eq 'fix_patch' || $mapType eq 'novel_patch') {
+    if ($mapType eq 'haplotype' || $mapType eq 'fix_patch' || $mapType eq 'novel_patch' || $mapType eq 'patch') {
       my $gbAcc = $refMapping->findvalue('@other_id_syn');
       $gbAcc =~ m/^[A-Z]+\d+\.\d+$/ || die "$xmlIn: $assemblyPrefix has $mapType mapping with " .
         "other_id_syn='$gbAcc', expecting versioned GenBank acc (e.g. 'KI270850.1').";
       if ($assemblyPrefix eq 'GRCh37') {
         $gbAcc =~ s/\..*//;
         $gbAcc = lc $gbAcc;
       } else {
         $gbAcc =~ s/\./v/;
       }
       # Trim chromosome band stuff if present
       $seq =~ s/[pq].*//;
       if ($assemblyPrefix eq 'GRCh37' && exists $gbAccToHg19Alt{$gbAcc}) {
         $seq = $gbAccToHg19Alt{$gbAcc};
       } elsif ($seq eq 'Un') {
         $seq .= "_$gbAcc";