1dea84ee820d50f05255371bdaaf6d7b98f220ca
hiram
  Wed Mar 23 17:03:10 2022 -0700
adding construction of bigBed file for chromAlias refs #29111

diff --git src/hg/utils/automation/aliasTextToBed.pl src/hg/utils/automation/aliasTextToBed.pl
index 6383e70..f7fc41e 100755
--- src/hg/utils/automation/aliasTextToBed.pl
+++ src/hg/utils/automation/aliasTextToBed.pl
@@ -61,65 +61,75 @@
   $chromSizes{$chrom} = $size;
 }
 close (SZ);
 
 my %nameLabels = (
    "assembly" => "Assembly",
    "genbank" => "GenBank",
    "ncbi" => "NCBI",
    "refseq" => "RefSeq",
    "ucsc" => "UCSC",
    "ensembl" => "Ensembl"
 );
 
 open (AS, ">$opt_aliasAs") or die "can not write to $opt_aliasAs";
 
+my $indexNames;
+
 $titleLine =~ s/^#\s+//;
 my @legendNames = split('\s+', $titleLine);
 my $expectFieldCount = scalar(@legendNames);
 my $i = 0;
 # output the .as definition
 printf AS "table chromAlias\n";
 printf AS "   \"chromAlias bigBed index\"\n";
 printf AS "    (\n";
 printf AS "    string chrom;\t\"native sequence name\"\n";
 printf AS "    uint chromStart;\t\"always 0\"\n";
 printf AS "    uint chromEnd;\t\"chromosome size\"\n";
 foreach my $title (@legendNames) {
+  if (length($indexNames)) {
+    $indexNames .= "," . $title;
+  } else {
+    $indexNames = $title;
+  }
   printf AS "    string %s;\t\"%s name\"\n", $title, $nameLabels{$title};
 }
 printf AS "    )\n";
 close (AS);
 
+printf STDERR "# indexNames: '%s'\n", $indexNames;
+
 open (BD, ">$opt_aliasBed") or die "can not write to $opt_aliasBed";
 
 while (my $line = <FH>) {
   chomp $line;
   my @a = split('\t', $line, -1); # the -1 keeps all empty fields too
   if (scalar(@a) != $expectFieldCount) {
      printf STDERR "ERROR: expected field count %d =! %d on line %d\n", $expectFieldCount, scalar(@a), $.;
      exit 255;
   }
   my $nameIndex = 0;
   printf BD "%s\t0\t%d", $a[$nameIndex], $chromSizes{$a[$nameIndex]};
   foreach my $name (@a) {
     printf BD "\t%s", $a[$nameIndex++];
   }
   printf BD "\n";
 }
 close (FH);
 close (BD);
 
-print `bedToBigBed -tab -type=bed3+5 -as=$opt_aliasAs -extraIndex=ucsc,assembly,genbank,ncbi,refseq $opt_aliasBed $opt_chromSizes $opt_aliasBigBed`;
+printf STDERR "bedToBigBed -tab -type=bed3+5 -as=$opt_aliasAs -extraIndex=$indexNames $opt_aliasBed $opt_chromSizes $opt_aliasBigBed\n";
+print `bedToBigBed -tab -type=bed3+5 -as=$opt_aliasAs -extraIndex=$indexNames $opt_aliasBed $opt_chromSizes $opt_aliasBigBed`;
 
 __END__
 
 # ucsc	assembly	genbank	ncbi	refseq
 NW_011332701v1_alt	HG2139_PATCH	KN538374.1		NW_011332701.1
 chr1	1	CM000663.2	1	NC_000001.11
 chr10	10	CM000672.2	10	NC_000010.11
 chr10_NT_187579v1_alt	HSCHR10_1_CTG3	KI270824.1		NT_187579.1
 chr10_NT_187580v1_alt	HSCHR10_1_CTG4	KI270825.1		NT_187580.1
 chr10_NW_003315934v1_alt	HSCHR10_1_CTG1	GL383545.1		NW_003315934.1
 chr10_NW_003315935v1_alt	HSCHR10_1_CTG2	GL383546.1		NW_003315935.1
 chr10_NW_009646202v1_alt	HG2191_PATCH	KN196480.1		NW_009646202.1
 chr10_NW_011332692v1_alt	HG2241_PATCH	KN538365.1		NW_011332692.1