33b5cb286a820d589a23e013a66f8c401c3682bd
hiram
  Tue Aug 25 16:44:36 2020 -0700
better naming of the alias elements to see their names in the track refs #24396

diff --git src/hg/utils/automation/chromAliasBedTest.pl src/hg/utils/automation/chromAliasBedTest.pl
index b6a7894..24c53f4 100755
--- src/hg/utils/automation/chromAliasBedTest.pl
+++ src/hg/utils/automation/chromAliasBedTest.pl
@@ -1,66 +1,66 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 1) {
   printf STDERR "usage: chromAliasBedTest.pl <db> > chromAlias.<db>.bed\n";
   printf STDERR "writes to STDOUT a bed file that has every chrom name\n";
   exit 255;
 }
 # +----------+------------------+------+-----+---------+-------+
 # | Field    | Type             | Null | Key | Default | Extra |
 # +----------+------------------+------+-----+---------+-------+
 # | chrom    | varchar(255)     | NO   | PRI | NULL    |       |
 # | size     | int(10) unsigned | NO   |     | NULL    |       |
 # | fileName | varchar(255)     | YES  |     | NULL    |       |
 # +----------+------------------+------+-----+---------+-------+
 
 my $db = shift;
 
 my %chromSizes;	# key is chrom value is size
 open (FH, "hgsql -N -e 'select * from chromInfo;' $db|") or die "can not hgsql select from chromInfo.$db";
 while (my $line = <FH>) {
   chomp $line;
   my ($chrom, $size, $fileName) = split('\s+', $line);
   $chromSizes{$chrom} = $size;
 }
 close (FH);
 
 # foreach my $chr (sort keys %chromSizes) {
 #   printf "%s\t%d\n", $chr, $chromSizes{$chr};
 # }
 
 my %chromAlias;	#	key is external name value is UCSC name
 
 open (FH, "hgsql -N -e 'select * from chromAlias;' $db|") or die "can not hgsql select from chromAlias.$db";
 while (my $line = <FH>) {
   chomp $line;
   my ($external, $ucsc) = split('\s+', $line);
   $chromAlias{$external} = $ucsc;
 }
 close (FH);
 
 # output bed item for each external name
 my %ucscUsed;	# key is UCSC name, value is csv list of external names
 foreach my $external (sort keys %chromAlias) {
   my $ucscName = $chromAlias{$external};
-  printf "%s\t0\t%s\t%s\n", $external, $chromSizes{$ucscName}, $ucscName;
+  printf "%s\t0\t%s\t%s\n", $external, $chromSizes{$ucscName}, $external;
   if (defined($ucscUsed{$ucscName})) {
     $ucscUsed{$ucscName} .= "," . $external;
   } else {
     $ucscUsed{$ucscName} = $external;
   }
 }
 
 # catch up for those UCSC names not mentioned in chromAlias
 foreach my $ucscName (sort keys %chromSizes) {
   if (!defined($ucscUsed{$ucscName})) {
     printf "%s\t0\t%s\tnoAlias\n", $ucscName, $chromSizes{$ucscName};
   } else {
     printf "%s\t0\t%s\t%s\n", $ucscName, $chromSizes{$ucscName}, $ucscUsed{$ucscName};
   }
 }