790b166f17ba0ef2f8cfe220dbc6c2a67035ede9
hiram
  Wed Mar 15 21:16:40 2023 -0700
adding HPRC links to the index pages refs #30508

diff --git src/hg/makeDb/doc/asmHubs/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl
index 2b0a2f6..8b8b7b9 100755
--- src/hg/makeDb/doc/asmHubs/trackData.pl
+++ src/hg/makeDb/doc/asmHubs/trackData.pl
@@ -1,667 +1,690 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use File::Basename;
 use FindBin qw($Bin);
 use lib "$Bin";
 use commonHtml;
 use File::stat;
 
 my $argc = scalar(@ARGV);
 if ($argc < 3) {
   printf STDERR "usage: trackData.pl Name asmHubName [two column name list] > trackData.html\n";
   printf STDERR "e.g.: trackData.pl Mammals mammals mammals.asmId.commonName.tsv > trackData.html\n";
   printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n";
   printf STDERR "\nthe two columns are 1: asmId (accessionId_assemblyName)\n";
   printf STDERR "column 2: common name for species, columns separated by tab\n";
   exit 255;
 }
 
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 
 my $testOutput = 0;
 my $spliceOut = -1;
 
 if ($argc > 2) {
   for (my $i = 0; $i < $argc; ++$i) {
     if ($ARGV[$i] =~ /-test/) {
       $testOutput = 1;
       $spliceOut = $i;
     }
   }
 }
 if ($spliceOut != -1) {
   splice @ARGV, $spliceOut, 1;
 }
 my $Name = shift;
 my $asmHubName = shift;
 my $inputList = shift;
 my $orderList = $inputList;
 if ( ! -s "$orderList" ) {
   $orderList = $toolsDir/$inputList;
 }
 
 my @orderList;	# asmId of the assemblies in order from the orderList file
 my %commonName;	# key is asmId, value is a common name, perhaps more appropriate
                 # than found in assembly_report file
 		# assembly_report
 my $vgpIndex = 0;
 $vgpIndex = 1 if ($Name =~ m/vgp/i);
+my $hprcIndex = 0;
+$hprcIndex = 1 if ($Name =~ m/hprc/i);
 
 my $assemblyTotal = 0;	# complete list of assemblies in this group
 my $asmCount = 0;	# count of assemblies completed and in the table
 my $overallNucleotides = 0;
 my $overallSeqCount = 0;
 my $overallGapSize = 0;
 my $overallGapCount = 0;
 
 ##############################################################################
 # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
 ##############################################################################
 sub commify($) {
     my $text = reverse $_[0];
     $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
     return scalar reverse $text
 }
 
 # ($itemCount, $percentCover) = bigWigMeasure($trackFile, $genomeSize);
 sub bigWigMeasure($$) {
   my ($file, $genomeSize) = @_;
   my $bigWigInfo = `bigWigInfo "$file" | egrep "basesCovered:|mean:" | awk '{print \$NF}' | xargs echo | sed -e 's/,//g;'`;
   chomp $bigWigInfo;
   my ($bases, $mean) = split('\s+', $bigWigInfo);
   my $itemCount = sprintf ("%.2f", $mean);
   my $percentCover = sprintf("%.2f %%", 100.0 * $bases / $genomeSize);
   return ($itemCount, $percentCover);
 }
 
 # $percentCover = pcFbFile($trackFb);
 sub pcFbFile($) {
   my ($trackFb) = @_;
   my ($itemBases, undef, undef, $noGapSize, undef) = split('\s+', `cat $trackFb`, 5);
   my $percentCover = sprintf("%.2f %%", 100.0 * $itemBases / $noGapSize);
   return $percentCover;
 }
 
 # ($itemCount, $percentCover) = oneTrackData($asmId, $track, $trackFile, $totalSize, $trackFb, $runDir);
 # might have a track feature bits file (trackFb), maybe not
 sub oneTrackData($$$$$$) {
   my ($asmId, $trackName, $file, $genomeSize, $trackFb, $runDir) = @_;
 # printf STDERR "# %s\n", $file;
   my $itemCount = 0;
   my $percentCover = 0;
   if (! -s "${file}") {
     if ($trackName eq "gapOverlap") {
       if (-s "${runDir}/$asmId.gapOverlap.bed.gz" ) {
        my $lineCount=`zcat "${runDir}/$asmId.gapOverlap.bed.gz" | head | wc -l`;
         chomp $lineCount;
        if (0 == $lineCount) {
          return("0", "0 %");
        } else {
          return("n/a", "n/a");
        }
       }
     } elsif ($trackName eq "gap") {
       return("0", "0 %");
     } else {
       return("n/a", "n/a");
     }
   } else {
     if ($file =~ m/.bw$/) {
       ($itemCount, $percentCover) = bigWigMeasure($file, $genomeSize);
     } else {
       my $bigBedInfo = `bigBedInfo "$file" | egrep "itemCount:|basesCovered:" | awk '{print \$NF}' | xargs echo | sed -e 's/,//g;'`;
       chomp $bigBedInfo;
       my ($items, $bases) = split('\s', $bigBedInfo);
       $itemCount = commify($items);
       $percentCover = sprintf("%.2f %%", 100.0 * $bases / $genomeSize);
       if ( -s "${trackFb}" ) {
 	$percentCover = pcFbFile($trackFb);
       }
 # printf STDERR "# bigBedInfo %s %s %s\n", $itemCount, $percentCover, $file;
     }
   }
   return ($itemCount, $percentCover);
 }	#	sub oneTrackData($$$$$$)
 
 ##############################################################################
 ### start the HTML output
 ##############################################################################
 sub startHtml() {
 
 my $timeStamp = `date "+%F"`;
 chomp $timeStamp;
 
 my $subSetMessage = "subset of $asmHubName only";
 if ($asmHubName eq "vertebrate") {
    $subSetMessage = "subset of other ${asmHubName}s only";
 }
 
 if ($vgpIndex) {
   my $vgpSubset = "(set of primary assemblies)";
   if ($orderList =~ m/vgp.alternate/) {
      $vgpSubset = "(set of alternate/haplotype assemblies)";
   } elsif ($orderList =~ m/vgp.trio/) {
      $vgpSubset = "(set of trio assemblies, maternal/paternal)";
   } elsif ($orderList =~ m/vgp.legacy/) {
      $vgpSubset = "(set of legacy/superseded assemblies)";
   }
   print <<"END"
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="VGP - Vertebrate Genomes Project assembly hubs, track statistics" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>VGP - Vertebrate Genomes Project assembly hubs, track statistics</h1>
 <p>
 <a href='https://vertebrategenomesproject.org/' target=_blank>
 <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p>
 <p>
 This assembly hub contains assemblies released
 by the <a href='https://vertebrategenomesproject.org/' target=_blank>
 Vertebrate Genomes Project.</a> $vgpSubset
 </p>
 
 END
 } else {
+  if ($hprcIndex) {
+    print <<"END"
+<!DOCTYPE HTML 4.01 Transitional>
+<!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium assembly hubs, track statistics" -->
+<!--#set var="ROOT" value="../.." -->
+
+<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
+
+<h1>HPRC - Human Pangenome Reference Consortium assembly hubs, track statistics</h1>
+<p>
+<a href='https://humanpangenome.org/' target=_blank>
+<img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p>
+<p>
+This assembly hub contains assemblies released
+by the <a href='https://humanpangenome.org/' target=_blank>
+Human Pangenome Reference Consortium.</a>
+</p>
+
+END
+  } else {
     print <<"END"
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="$Name genomes assembly hubs, track statistics" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>$Name Genomes assembly hubs, track statistics</h1>
 <p>
 Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
 </p>
 
 END
   }
+}
   my $indexUrl = "index";
   my $asmStats = "asmStats";
   print <<"END"
 <h3>See also: <a href='$indexUrl.html'>hub access</a>,&nbsp;<a href='$asmStats.html'>assembly statistics</a></h3><br>
 
 <h3>Data resource links</h3>
 NOTE: <em>Click on the column headers to sort the table by that column</em><br>
 The <em>link to genome browser</em> will attach only that single assembly to
 the genome browser.<br>
 The numbers are: item count (percent coverage)<br>
 Except for the gc5Base column which is: overall GC % average (percent coverage)
 END
 }	#	sub startHtml()
 
 # order of columns in the table
 # eliminated the ncbiGene track
 my @trackList = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base allGaps assembly rmsk simpleRepeat windowMasker cpgIslandExtUnmasked);
 ### XXX beware, this trackList is going to be edited below to add or
 ###             remove elements depending upon the situation
 
 ##############################################################################
 ### start the table output
 ##############################################################################
 sub startTable() {
 
 # coordinate the order of these column headings with the @trackList listed above
 
 print '<table class="sortable" border="1">
 <thead><tr><th>count</th>
   <th>common name<br>link&nbsp;to&nbsp;genome&nbsp;browser</th>
 ';
   print '<th class="sorttable_numeric">ncbiRefSeq</th>
 ' if ("viral" ne $asmHubName);
 
 print "  <th class=\"sorttable_numeric\">ncbiGene</th>\n" if ($testOutput || ("viral" eq $asmHubName));
 
 print '  <th class="sorttable_numeric">xenoRefGene</th>
   <th class="sorttable_numeric">augustus<br>genes</th>
   <th class="sorttable_numeric">Ensembl<br>genes</th>
 ' if ("viral" ne $asmHubName);
 
 print '  <th class="sorttable_numeric">gc5 base</th>
 ';
 
 if ($testOutput) {
   print "  <th class=\"sorttable_numeric\">AGP<br>gap</th>\n";
   print "  <th class=\"sorttable_numeric\">all<br>gaps</th>\n";
 } else {
   print "  <th class=\"sorttable_numeric\">gaps</th>\n";
 }
 
 print '  <th class="sorttable_numeric">assembly<br>sequences</th>
   <th class="sorttable_numeric">Repeat<br>Masker</th>
   <th class="sorttable_numeric">TRF<br>simpleRepeat</th>
   <th class="sorttable_numeric">window<br>Masker</th>
 ';
 
 if ($testOutput) {
 print '  <th class="sorttable_numeric">gap<br>Overlap</th>
   <th class="sorttable_numeric">tandem<br>Dups</th>
   <th class="sorttable_numeric">cpg<br>unmasked</th>
   <th class="sorttable_numeric">cpg<br>island</th>
 ';
 
 } else {
   print "  <th class=\"sorttable_numeric\">cpg<br>islands</th>\n";
 }
 
 print "</tr></thead><tbody>\n";
 }	#	sub startTable()
 
 ##############################################################################
 ### end the table output
 ##############################################################################
 sub endTable() {
 
 my $commaNuc = commify($overallNucleotides);
 my $commaSeqCount = commify($overallSeqCount);
 my $commaGapSize = commify($overallGapSize);
 my $commaGapCount = commify($overallGapCount);
 
 my $percentDone = 100.0 * $asmCount / $assemblyTotal;
 my $doneMsg = "";
 if ($asmCount < $assemblyTotal) {
   $doneMsg = sprintf(" (%d build completed, %.2f %% finished)", $asmCount, $percentDone);
 }
 my $columnCount = scalar(@trackList);
 my $colSpanFill = $columnCount - 1;
 
 if ($assemblyTotal > 1) {
   print <<"END"
 
 </tbody>
 <tfoot><tr><th>TOTALS:</th><td align=center colspan=$colSpanFill>total assembly count&nbsp;${assemblyTotal}${doneMsg}</td>
   </tr></tfoot>
 </table>
 END
 } else {
   print <<"END"
 
 </tbody>
 </table>
 END
 }
 }	#	sub endTable()
 
 ##############################################################################
 ### end the HTML output
 ##############################################################################
 sub endHtml() {
 
 &commonHtml::otherHubLinks($vgpIndex, $asmHubName);
 &commonHtml::htmlFooter($vgpIndex, $asmHubName);
 
 }	#	sub endHtml()
 
 sub asmCounts($) {
   my ($chromSizes) = @_;
   my ($sequenceCount, $totalSize) = split('\s+', `ave -col=2 $chromSizes | egrep "^count|^total" | awk '{printf "%d\\n", \$NF}' | xargs echo`);
   return ($sequenceCount, $totalSize);
 }
 
 sub maskStats($) {
   my ($faSizeFile) = @_;
   my $sizeNoGaps = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$4}'`;
   my $gapSize = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$3}'`;
   chomp $gapSize;
   $gapSize =~ s/\(//;
   my $totalBases = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$1}'`;
   chomp $totalBases;
   my $maskedBases = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$9}'`;
   chomp $maskedBases;
   my $maskPerCent = 100.0 * $maskedBases / $totalBases;
   return ($gapSize, $maskPerCent, $sizeNoGaps);
 }
 
 # grep "sequences in 1 file" GCA_900324465.2_fAnaTes1.2.faSize.txt
 # 555641398 bases (3606496 N's 552034902 real 433510637 upper 118524265 lower) in 50 sequences in 1 files
 
 sub gapStats($$) {
   my ($buildDir, $asmId) = @_;
   my $gapBed = "$buildDir/trackData/allGaps/$asmId.allGaps.bed.gz";
   my $gapCount = 0;
   if ($asmId !~ m/^GC/) {
      $gapBed = "/hive/data/genomes/$asmId/$asmId.N.bed";
      if ( -s "$gapBed" ) {
        $gapCount = `awk '{print \$3-\$2}' $gapBed | ave stdin | grep '^count' | awk '{print \$2}'`;
      }
   } elsif ( -s "$gapBed" ) {
     $gapCount = `zcat $gapBed | awk '{print \$3-\$2}' | ave stdin | grep '^count' | awk '{print \$2}'`;
   }
   chomp $gapCount;
   return ($gapCount);
 }
 
 ##############################################################################
 ### tableContents()
 ##############################################################################
 sub tableContents() {
   my $asmCounted = 0;
   if ($testOutput) {  # add extra columns during 'test' output
 #                       0          1          2        3       4      5    6
 #  7       8      9            10           11        12          13
 #     14
 # my @trackList = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base gap allGaps assembly rmsk simpleRepeat windowMasker gapOverlap tandemDups cpgIslandExtUnmasked cpgIslandExt);
 #                       0            1         2        3       4      5      6
 #      7      8           9               10
 # my @trackList = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base allGaps assembly rmsk simpleRepeat windowMasker cpgIslandExtUnmasked);
     splice @trackList, 11, 0, "cpgIslandExt";
     splice @trackList, 10, 0, "tandemDups";
     splice @trackList, 10, 0, "gapOverlap";
     splice @trackList, 5, 0, "gap";
   }
   if ("viral" eq $asmHubName) {
     splice @trackList, 3, 1;
     splice @trackList, 2, 1;
     splice @trackList, 1, 1;
   }
   if ($testOutput || ("viral" eq $asmHubName)) {  # add extra columns during 'test' output
     splice @trackList, 1, 0, "ncbiGene";
   }
   if ("viral" eq $asmHubName) {
     splice @trackList, 0, 1;
   }
   foreach my $asmId (@orderList) {
     my $gcPrefix = "GCx";
     my $asmAcc = "asmAcc";
     my $asmName = "asmName";
     my $accessionId = "GCx_098765432.1";
     my $accessionDir = "";
     my $configRa = "n/a";
     my $tracksCounted = 0;
     my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
     my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
     my $chromSizes = "${buildDir}/${asmId}.chrom.sizes";
     my $twoBit = "${buildDir}/trackData/addMask/${asmId}.masked.2bit";
     my $faSizeTxt = "${buildDir}/${asmId}.faSize.txt";
     if ($asmId !~ m/^GC/) {
        $configRa = "/hive/data/genomes/$asmId/$asmId.config.ra";
       $accessionId = `grep ^genBankAccessionID "${configRa}" | cut -d' ' -f2`;
        chomp $accessionId;
        $asmName = `grep ^ncbiAssemblyName "${configRa}" | cut -d' ' -f2`;
        chomp $asmName;
        $accessionDir = substr($accessionId, 0 ,3);
        $accessionDir .= "/" . substr($accessionId, 4 ,3);
        $accessionDir .= "/" . substr($accessionId, 7 ,3);
        $accessionDir .= "/" . substr($accessionId, 10 ,3);
        ($gcPrefix, $asmAcc) = split('_', $accessionId, 2);
        $buildDir="/hive/data/outside/ncbi/genomes/$accessionDir/${accessionId}_${asmName}";
        $asmReport="$buildDir/${accessionId}_${asmName}_assembly_report.txt";
        $chromSizes = "/hive/data/genomes/$asmId/chrom.sizes";
        $twoBit = "/hive/data/genomes/$asmId/$asmId.2bit";
        $faSizeTxt = "/hive/data/genomes/$asmId/faSize.${asmId}.2bit.txt";
     } else {
        ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3);
        $accessionId = sprintf("%s_%s", $gcPrefix, $asmAcc);
        $accessionDir = substr($asmId, 0 ,3);
        $accessionDir .= "/" . substr($asmId, 4 ,3);
        $accessionDir .= "/" . substr($asmId, 7 ,3);
        $accessionDir .= "/" . substr($asmId, 10 ,3);
       $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
        if ($gcPrefix eq "GCA") {
      $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId";
        }
        $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
        $chromSizes = "${buildDir}/${asmId}.chrom.sizes";
        $twoBit = "${buildDir}/trackData/addMask/${asmId}.masked.2bit";
        $faSizeTxt = "${buildDir}/${asmId}.faSize.txt";
     }
 #    my $trackDb="$buildDir/${asmId}.trackDb.txt";
 #    next if (! -s "$trackDb");	# assembly build not complete
     if (! -s "$asmReport") {
       printf STDERR "# no assembly report:\n# %s\n", $asmReport;
       next;
     }
     if (! -s "$twoBit") {
       printf STDERR "# no 2bit file:\n# %s\n", $twoBit;
       printf "<tr><td align=right>%d</td>\n", ++$asmCount;
       printf "<td align=center>%s</td>\n", $accessionId;
       printf "<th colspan=15 align=center>missing masked 2bit file</th>\n";
       printf "</tr>\n";
       next;
     }
     if ( ! -s "$faSizeTxt" ) {
        printf STDERR "twoBitToFa $twoBit stdout | faSize stdin > $faSizeTxt\n";
        print `twoBitToFa $twoBit stdout | faSize stdin > $faSizeTxt`;
     }
     my ($gapSize, $maskPerCent, $sizeNoGaps) = maskStats($faSizeTxt);
     $overallGapSize += $gapSize;
     my ($seqCount, $totalSize) = asmCounts($chromSizes);
     $overallSeqCount += $seqCount;
     $overallNucleotides += $totalSize;
     my $gapCount = gapStats($buildDir, $asmId);
     $overallGapCount += $gapCount;
     my $sciName = "notFound";
     my $commonName = "notFound";
     my $asmDate = "notFound";
     my $itemsFound = 0;
     open (FH, "<$asmReport") or die "can not read $asmReport";
     while (my $line = <FH>) {
       last if ($itemsFound > 5);
       chomp $line;
       $line =~ s/
//g;;
       $line =~ s/\s+$//g;;
       if ($line =~ m/Date:/) {
         if ($asmDate =~ m/notFound/) {
            ++$itemsFound;
            $asmDate = $line;
            $asmDate =~ s/.*:\s+//;
         }
       } elsif ($line =~ m/Organism name:/) {
         if ($sciName =~ m/notFound/) {
            ++$itemsFound;
            $commonName = $line;
            $sciName = $line;
            $commonName =~ s/.*\(//;
            $commonName =~ s/\)//;
            $commonName = $commonName{$asmId} if (exists($commonName{$asmId}));
            $sciName =~ s/.*:\s+//;
            $sciName =~ s/\s+\(.*//;
         }
       }
     }
     close (FH);
     my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId";
     my $browserName = $commonName;
     my $browserUrl = "https://genome.ucsc.edu/h/$accessionId";
     if ($asmId !~ m/^GC/) {
        $hubUrl = "https://hgdownload.soe.ucsc.edu/goldenPath/$asmId/bigZips";
        $browserUrl = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=$asmId";
        $browserName = "$commonName ($asmId)";
        if ($testOutput) {
          $browserUrl = "https://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=$asmId";
          $hubUrl = "https://hgdownload-test.gi.ucsc.edu/goldenPath/$asmId/bigZips";
        }
     } elsif ($testOutput) {
       $browserUrl = "https://genome-test.gi.ucsc.edu/h/$accessionId";
     }
     printf "<tr><td align=right>%d</td>\n", ++$asmCount;
     printf "<td align=center><a href='%s' target=_blank>%s<br>%s</a></td>\n", $browserUrl, $browserName, $accessionId;
     foreach my $track (@trackList) {
       my $trackFile = "$buildDir/bbi/$asmId.$track";
       my $trackFb = "$buildDir/trackData/$track/fb.$asmId.$track.txt";
       my $runDir = "$buildDir/trackData/$track";
       my ($itemCount, $percentCover);
       my $customKey = "";
       if ($asmId !~ m/^GC/) {
         $itemCount = "n/a";
         $percentCover = "n/a";
         if ($track eq "ncbiRefSeq") {
           my $refSeqDir=`ls -d /hive/data/genomes/$asmId/bed/ncbiRefSeq.20* | tail -1`;
           chomp $refSeqDir;
           if ( -d "${refSeqDir}" ) {
             my $trackFb = "${refSeqDir}/fb.ncbiRefSeq.$asmId.txt";
             if ( -s "${trackFb}" ) {
               $itemCount = `hgsql -N -e 'select count(*) from $track;' $asmId 2> /dev/null`;
               chomp $itemCount;
               $percentCover = pcFbFile($trackFb);
             }
           }
         } elsif ($track eq "gc5Base") {
           my $bwFile = "/gbdb/$asmId/bbi/gc5Base.bw";
         $bwFile = "/gbdb/$asmId/bbi/gc5BaseBw/gc5Base.bw" if (! -s "${bwFile}");
           ($itemCount, $percentCover) = bigWigMeasure($bwFile, $totalSize);
         } elsif ($track eq "rmsk") {
           my $rmskStats = "/hive/data/genomes/$asmId/bed/repeatMasker/$asmId.rmsk.stats";
           if (! -s "${rmskStats}") {
             my $faOut = "/hive/data/genomes/$asmId/bed/repeatMasker/$asmId.sorted.fa.out.gz";
             if ( -s "$faOut") {
 		my $items = `zgrep -c ^ "$faOut"`;
 		chomp $items;
 		$itemCount = commify($items);
 		my $masked = `grep masked "/hive/data/genomes/$asmId/bed/repeatMasker/faSize.rmsk.txt" | awk '{print \$4}' | sed -e 's/%//;'`;
 		chomp $masked;
 		$percentCover = sprintf("%.2f %%", $masked);
 		open (RS, ">$rmskStats") or die "can now write to $rmskStats";
 		printf RS "%s\t%s\n", $itemCount, $percentCover;
 		close (RS);
 	    } else {
 		$itemCount = "n/a";
 		$percentCover = "n/a";
             }
           } else {
             ($itemCount, $percentCover) = split('\s+', `cat $rmskStats`);
             chomp $percentCover;
             $customKey = sprintf("%.2f", $percentCover);
             $percentCover = sprintf("%.2f %%", $percentCover);
           }
         }	# elsif ($track eq "rmsk")
 ########### need to figure which tables can be measured here
 #        x else x
 #          $itemCount = `hgsql -N -e 'select count(*) from $track;' $asmId 2> /dev/null`;
 #          chomp $itemCount;
 #          if (length($itemCount) < 1) {
 #	    $itemCount = "n/a";
 #	    $percentCover = "n/a";
 #          } else {
 #            $percentCover = `featureBits $asmId $track 2>&1 | cut -d' ' -f5 | tr -d ')('`;
 #            chomp $percentCover;
 #            $customKey = $percentCover;
 #            $customKey =~ s/[ %]+//;
 #          }
       } else {	# working on an assembly hub
 	if ( "$track" eq "gc5Base" ) {
           $trackFile .= ".bw";
 	} else {
           $trackFile .= ".bb";
 	}
 	if ( "$track" eq "rmsk") {
           my $rmskStats = "$buildDir/trackData/repeatMasker/$asmId.rmsk.stats";
           if (! -s "${rmskStats}") {
             my $faOut = "$buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz";
             if ( -s "$faOut") {
                 my $items = `zgrep -c ^ "$faOut"`;
                 chomp $items;
                 $itemCount = commify($items);
                 my $masked = `grep masked "$buildDir/trackData/repeatMasker/faSize.rmsk.txt" | awk '{print \$4}' | sed -e 's/%//;'`;
                 chomp $masked;
                 $percentCover = sprintf("%.2f %%", $masked);
                 open (RS, ">$rmskStats") or die "can now write to $rmskStats";
                 printf RS "%s\t%s\n", $itemCount, $percentCover;
                 close (RS);
             } else {
                 $itemCount = "n/a";
                 $percentCover = "n/a";
             }
           } else {
             ($itemCount, $percentCover) = split('\s+', `cat $rmskStats`);
             chomp $percentCover;
             $customKey = sprintf("%.2f", $percentCover);
             $percentCover = sprintf("%.2f %%", $percentCover);
           }
 	} else {	# not the rmsk track
           ($itemCount, $percentCover) = oneTrackData($asmId, $track, $trackFile, $totalSize, $trackFb, $runDir);
           if (0 == $testOutput) {
               # if track ncbiRefSeq does not exist, try the ncbiGene track
             if ($track eq "ncbiRefSeq" && $itemCount eq "n/a") {
               $runDir = "$buildDir/trackData/ncbiGene";
               $trackFile = "$buildDir/bbi/$asmId.$track.bb";
               ($itemCount, $percentCover) = oneTrackData($asmId, "ncbiGene", $trackFile, $totalSize, $trackFb, $runDir);
             }
           }
 	}	#       else not the rmsk track
       }		#       else if ($asmId !~ m/^GC/)
       if (($percentCover =~ m/%/) || ($percentCover !~ m#n/a#)) {
         $customKey = $percentCover;
         $customKey =~ s/[ %]+//;
       }
       if (length($customKey)) {
         printf "    <td align=right sorttable_customkey='%s'>%s<br>(%s)</td>\n", $customKey, $itemCount, $percentCover;
       } else {
         if ($itemCount eq "n/a") {
       printf "    <td align=right>n/a</td>\n";
         } else {
       printf "    <td align=right>%s<br>(%s)</td>\n", $itemCount, $percentCover;
         }
       }
       $tracksCounted += 1 if ($itemCount ne "n/a");
     }	#	foreach my $track (@trackList)
     printf "</tr>\n";
     $asmCounted += 1;
     if ($asmId =~ m/^GC/) {
        printf STDERR "# %03d\t%02d tracks\t%s\n", $asmCounted, $tracksCounted, $asmId;
     } else {
        printf STDERR "# %03d\t%02d tracks\t%s_%s (%s)\n", $asmCounted, $tracksCounted, $accessionId, $asmName, $asmId;
     }
   }
 }
 
 ##############################################################################
 ### main()
 ##############################################################################
 
 # if there is a 'promoted' list, it has been taken out of the 'orderList'
 # so will need to stuff it back in at the correct ordered location
 my %promotedList;	# key is asmId, value is common name
 my $promotedList = dirname(${orderList}) . "/promoted.list";
 my @promotedList;	# contents are asmIds, in order by lc(common name)
 my $promotedIndex = -1;	# to walk through @promotedList;
 
 if ( -s "${promotedList}" ) {
   open (FH, "<${promotedList}" ) or die "can not read ${promotedList}";
   while (my $line = <FH>) {
     next if ($line =~ m/^#/);
     chomp $line;
     my ($asmId, $commonName) = split('\t', $line);
     $promotedList{$asmId} = $commonName;
   }
   close (FH);
   foreach my $asmId ( sort { lc($promotedList{$a}) cmp lc($promotedList{$b}) } keys %promotedList) {
      push @promotedList, $asmId;
   }
   $promotedIndex = 0;
 }
 
 open (FH, "<${orderList}") or die "can not read ${orderList}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($asmId, $commonName) = split('\t', $line);
   if ( ($promotedIndex > -1) && ($promotedIndex < scalar(@promotedList))) {
      my $checkInsertAsmId = $promotedList[$promotedIndex];
      my $checkInsertName = $promotedList{$checkInsertAsmId};
      # insert before this commonName when alphabetic before
      if (lc($checkInsertName) lt lc($commonName)) {
        push @orderList, $checkInsertAsmId;
        $commonName{$checkInsertAsmId} = $checkInsertName;
        ++$assemblyTotal;
        printf STDERR "# inserting '%s' before '%s' at # %03d\n", $checkInsertName, $commonName, $assemblyTotal;
        ++$promotedIndex;	# only doing one at this time
                         # TBD: will need to improve this for more inserts
      }
   }
   push @orderList, $asmId;
   $commonName{$asmId} = $commonName;
   ++$assemblyTotal;
 }
 close (FH);
 
 startHtml();
 startTable();
 tableContents();
 endTable();
 endHtml();