5c41c93386c2b2b36bd68423799d197e9c49675a
galt
  Wed May 12 00:07:13 2021 -0700
oops. mm10 does not need lower-case IDs.

diff --git src/hg/utils/automation/altScaffoldPlacementToBed.pl src/hg/utils/automation/altScaffoldPlacementToBed.pl
index b56c0a9..45c8ff6 100755
--- src/hg/utils/automation/altScaffoldPlacementToBed.pl
+++ src/hg/utils/automation/altScaffoldPlacementToBed.pl
@@ -38,41 +38,45 @@
   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/ || $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)";
+      if ($opt_db && ($opt_db eq 'hg19')) {
 	$chr = lc($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)";
+    if ($opt_db && ($opt_db eq 'hg19')) {
       $altAcc = lc($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";
 }