037a404d5b76d3005d0263ef6212066e3073ea4a
galt
  Fri Apr 23 02:27:58 2021 -0700
altScaffoldPlacementToBed.pl handle MMCHR scaffold fix on alt for mouse.

diff --git src/hg/utils/automation/altScaffoldPlacementToBed.pl src/hg/utils/automation/altScaffoldPlacementToBed.pl
index 136809f..b56c0a9 100755
--- src/hg/utils/automation/altScaffoldPlacementToBed.pl
+++ src/hg/utils/automation/altScaffoldPlacementToBed.pl
@@ -33,40 +33,45 @@
   close($F);
 }
 
 while (<>) {
   next if (/^#/);
   chomp;
   my @w = split("\t");
   my ($altScafName, $altAcc, $c, $cAcc, $altStart, $altEnd, $cStart, $cEnd, $altEndTail) =
        ($w[2], $w[3], $w[5], $w[6], $w[9], $w[10], $w[11], $w[12], $w[14]);
   my $suffix = $aNameToSuffix{$altScafName};
   if (! $suffix) {
     $suffix = ($altScafName =~ m/PATCH$/) ? "fix" : "alt";
   }
   my $chr = "chr$c";
   my $chrBase = $chr;
-  if ($c =~ m/^HSCHR/) {
+  if ($c =~ m/^HSCHR/ || $c =~ m/^MMCHR/) {
     # Mapping is not alt/fix to chrom, but fix to alt; convert alt accession to UCSC format:
     $chr = $cAcc;
     if ($opt_db && ($opt_db eq 'hg19' || $opt_db eq 'mm10')) {
       $chr =~ s/^(\w+)\.\d+/$1/ || die "Unexpected cAcc ($cAcc)";
       $chr = lc($chr);
     } else {
       $chr =~ s/^(\w+)\.(\d+)/$1v$2/ || die "Unexpected cAcc ($cAcc)";
     }
+    if ($c =~ m/^HSCHR/) {
       $chrBase =~ s/HSCHR([A-Z0-9]+)_.*/$1/;
+    }
+    if ($c =~ m/^MMCHR/) {
+      $chrBase =~ s/MMCHR([A-Z0-9]+)_.*/$1/;
+    }
     $chr = "${chrBase}_${chr}_alt";
   }
   if ($opt_db && ($opt_db eq 'hg19' || $opt_db eq 'mm10')) {
     $altAcc =~ s/^(\w+)\.\d+/$1/ || die "Unexpected altAcc ($altAcc)";
     $altAcc = lc($altAcc);
   } else {
     $altAcc =~ s/^(\w+)\.(\d+)/$1v$2/ || die "Unexpected altAcc ($altAcc)";
   }
   $altAcc = "${chrBase}_${altAcc}_$suffix";
   my $altName = $altAcc;
   if ($altStart > 1 || $altEndTail > 0) {
     $altName .= ":$altStart-$altEnd";
   }
   print join("\t", $chr, $cStart-1, $cEnd, $altName) . "\n";
   print join("\t", $altAcc, $altStart-1, $altEnd, $chr.":$cStart-$cEnd") . "\n";