5c6eeb845281a9cf407dcadd3480b1c65bfb48c7
hiram
  Wed Dec 21 11:00:05 2022 -0800
mistaken left on forced UCSC names for alt sequences no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 4e4ae60..1a77c0f 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -461,31 +461,31 @@
 }	# sub unlocalizedFasta($$$)
 
 #########################################################################
 # read alt_scaffold_placement file, return name correspondence in
 # given hash pointer
 sub readAltPlacement($$) {
   my ($altPlacementFile, $accToChr) = @_;
   open (AP, "<$altPlacementFile") or die "can not read $altPlacementFile";
   while (my $line = <AP>) {
     chomp $line;
     next if ($line =~ m/^#/);
     my ($alt_asm_name, $prim_asm_name, $alt_scaf_name, $alt_scaf_acc, $parent_type, $parent_name, $parent_acc, $region_name, $ori, $alt_scaf_start, $alt_scaf_stop, $parent_start, $parent_stop, $alt_start_tail, $alt_stop_tail) = split('\t', $line);
     my $acc = $alt_scaf_acc;
     $alt_scaf_acc = $acc;
     my $ucscName = $acc;
-    if (1 == 1 || $ucscNames) {
+    if ($ucscNames) {
       $alt_scaf_acc =~ s/\./v/;
       $ucscName = sprintf("chr%s_%s_alt", $parent_name, $alt_scaf_acc);
       if ( $prim_asm_name ne "Primary Assembly" ) {
         $ucscName = sprintf("%s_alt", $alt_scaf_acc);
       }
     }
     $accToChr->{$acc} = $ucscName;
     printf STDERR "# warning: name longer than 31 characters: '%s'\n# in: '%s'\n", $ucscName, $altPlacementFile if (length($ucscName) > 31);
   }
   close (AP);
 }	#	sub readAltPlacement($$)
 
 #########################################################################
 ### process one of the alternate AGP files, changing names via the nameHash
 ### and writing to the given fileHandle (fh)