f3707c75a44a765397fd2c7f9144dc5dfd61f3c7
hiram
  Wed Aug 19 09:46:50 2026 -0700
restore the backslash r character which was lost in edits since it used to be an explicit control-M literal character found by claude code review no redmine

diff --git src/hg/makeDb/doc/asmHubs/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl
index 50f58aad6ab..26b44649f47 100755
--- src/hg/makeDb/doc/asmHubs/trackData.pl
+++ src/hg/makeDb/doc/asmHubs/trackData.pl
@@ -1,797 +1,797 @@
 #!/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 != 5) {
   printf STDERR "usage: trackData.pl Name asmHubName orderList prodOutFile testOutFile\n";
   printf STDERR "e.g.: trackData.pl Mammals mammals mammals.asmId.commonName.tsv trackData.html testTrackData.html\n";
   printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n";
   printf STDERR "\nthe two columns in the name list are 1: asmId (accessionId_assemblyName)\n";
   printf STDERR "column 2: common name for species, columns separated by tab\n";
   printf STDERR "\nWrites both the production and the '-test' variant of the track\n";
   printf STDERR "statistics page in a single pass over the assembly list -- each\n";
   printf STDERR "assembly's per-track stats (bigWigInfo/bigBedInfo/faSize etc.) are\n";
   printf STDERR "measured once and reused for both pages, instead of running the\n";
   printf STDERR "whole scan twice.\n";
   exit 255;
 }
 
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 my $sciNameOverrideFile = "$toolsDir/sciNameOverride.txt";
 my %sciNameOverride;	# key is accession, value is corrected scientific name
 my %taxIdOverride;	# key is accession, value is corrected taxId
 			# keys for both of those can also be the asmId
 
 if ( -s "${sciNameOverrideFile}" ) {
   open (my $sn, "<", "${sciNameOverrideFile}") or die "can not read ${sciNameOverrideFile}";
   while (my $line = <$sn>) {
     next if ($line =~ m/^#/);
     next if (length($line) < 2);
     chomp $line;
     my ($accO, $asmIdO, $sciNameO, $taxIdO) = split('\t', $line);
     $sciNameOverride{$accO} = $sciNameO;
     $sciNameOverride{$asmIdO} = $sciNameO;
     $taxIdOverride{$accO} = $taxIdO;
     $taxIdOverride{$asmIdO} = $taxIdO;
   }
   close ($sn);
 }
 
 my $Name = shift;
 my $asmHubName = shift;
 my $inputList = shift;
 my $prodOutFile = shift;
 my $testOutFile = 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 $brcIndex = 0;
 $brcIndex = 1 if ($Name =~ m/brc/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
 }
 
 ##############################################################################
 # capture(&): run a block of code that 'print's/'printf's, and return
 # everything it printed as a string, instead of letting it go to STDOUT.
 # This lets startHtml()/startTable()/endTable()/endHtml() keep their
 # original print-based bodies unchanged, while the caller decides which
 # of the two output files (or both) a given fragment belongs in.
 ##############################################################################
 sub capture(&) {
   my ($code) = @_;
   my $buf = '';
   open(my $fh, '>', \$buf) or die "capture: $!";
   my $old = select($fh);
   $code->();
   select($old);
   close($fh);
   return $buf;
 }
 
 # ($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 -- identical for the prod and -test pages
 ##############################################################################
 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>
 <!--#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>
 <!--#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
   } elsif ($brcIndex) {
     print <<"END";
 <!DOCTYPE HTML>
 <!--#set var="TITLE" value="BRC - Bioinformatics Research Center - track statistics" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>BRC - Bioinformatics Research Center - track statistics</h1>
 <p>
 <a href='https://brc-analytics.org/' target=_blank>
 <img src='BRClogo.svg' height=26 alt='BRC logo'></a></p>
 <p>
 This site will provide data access to genomes and annotations for all
 eukaryotic pathogens, host taxa, and vectors previously served by
 VEuPathDB. This is a part of the BRC Analytics project funded by the NIAID.
 For more information, see also:
 <a href=' https://brc-analytics.org' target=_blank>brc-analytics.org</a>
 </p>
 
 END
   } else {
     print <<"END"
 <!DOCTYPE HTML>
 <!--#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()
 
 ##############################################################################
 # buildTrackList($testOutput, $asmHubName): the order of columns in the
 # table, for either the production ($testOutput = 0) or -test ($testOutput
 # = 1) variant.  This used to be a single global array that tableContents()
 # mutated in place with these same splices, gated on a global $testOutput --
 # calling this twice (once per variant) instead reproduces both variants
 # exactly, without needing two separate runs of the script.
 ##############################################################################
 sub buildTrackList($$) {
   my ($testOutput, $asmHubName) = @_;
   # eliminated the ncbiGene track
   my @list = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base allGaps assembly rmsk simpleRepeat windowMasker cpgIslandExtUnmasked);
   if ($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 @list, 11, 0, "cpgIslandExt";
     splice @list, 10, 0, "tandemDups";
     splice @list, 10, 0, "gapOverlap";
     splice @list, 5, 0, "gap";
   }
   if ("viral" eq $asmHubName) {
     splice @list, 3, 1;
     splice @list, 2, 1;
     splice @list, 1, 1;
   }
   if ($testOutput || ("viral" eq $asmHubName)) {  # add extra columns during 'test' output
     splice @list, 1, 0, "ncbiGene";
   }
   if ("viral" eq $asmHubName) {
     splice @list, 0, 1;
   }
   return @list;
 }
 
 ##############################################################################
 ### start the table output
 ##############################################################################
 sub startTable($) {
   my ($testOutput) = @_;
 
 # coordinate the order of these column headings with buildTrackList() above
 
 print '<table class="sortable" border="1">
 <thead style="position:sticky; top:0;"><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 ($assemblyTotal, $asmCount, $columnCount) = @_;
 
 my $percentDone = 100.0 * $asmCount / $assemblyTotal;
 my $doneMsg = "";
 if ($asmCount < $assemblyTotal) {
   $doneMsg = sprintf(" (%d build completed, %.2f %% finished)", $asmCount, $percentDone);
 }
 my $colSpanFill = $columnCount - 1;
 
 if ($assemblyTotal > 1) {
   print <<"END"
 
 </tbody>
 <tfoot><tr><th>TOTALS:</th><td style='text-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 -- identical for the prod and -test pages
 ##############################################################################
 sub endHtml() {
 
 &commonHtml::otherHubLinks($vgpIndex, $asmHubName);
 &commonHtml::htmlFooter($vgpIndex, $asmHubName);
 
 }	#	sub endHtml()
 
 sub asmCounts($) {
   my ($chromSizes) = @_;
   my ($sequenceCount, $totalSize) = split('\s+', `/cluster/bin/x86_64/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}' $gapBed | /cluster/bin/x86_64/ave stdin | grep '^count' | awk '{print \$2}'`;
      }
   } elsif ( -s "$gapBed" ) {
     $gapCount = `zcat $gapBed | awk '{print \$3-\$2}' | /cluster/bin/x86_64/ave stdin | grep '^count' | awk '{print \$2}'`;
   }
   chomp $gapCount;
   return ($gapCount);
 }
 
 ##############################################################################
 # computeTrackCell($asmId, $track, $buildDir, $totalSize)
 # returns (itemCount, percentCover, customKey) for one track of one
 # assembly.  This is the expensive part (bigWigInfo/bigBedInfo/hgsql/etc.)
 # and is testOutput-independent, so it only needs to run once per assembly
 # per track no matter how many page variants reference that track.
 #
 # NOTE: the original script additionally retried a "still n/a" ensGene or
 # ncbiRefSeq track as ebiGene/ncbiGene, but on production output only. That
 # retry re-checked the *same* file path that had just been found missing
 # (only $runDir and the diagnostic track-name argument differed, and
 # oneTrackData() only consults $runDir for the unrelated 'gapOverlap' case)
 # -- so it was a guaranteed no-op and is not reproduced here.
 ##############################################################################
 sub computeTrackCell($$$$) {
   my ($asmId, $track, $buildDir, $totalSize) = @_;
   my $trackFile = "$buildDir/bbi/$asmId.$track";
   my $trackFb = "$buildDir/trackData/$track/fb.$asmId.$track.txt";
   # no ensGene file ?  Then look for ebiGene file
   if ($track eq "ensGene" && ! -s $trackFb) {
     if ( -d "$buildDir/trackData/ebiGene" ) {
       $trackFb = "$buildDir/trackData/ebiGene/fb.ebiGene.txt" if ( -d "$buildDir/trackData/ebiGene/fb.ebiGene.txt");
       $trackFile = "$buildDir/bbi/$asmId.ebiGene";
     }
   }
   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")
   } 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);
     }	#       else not the rmsk track
   }		#       else if ($asmId !~ m/^GC/)
   if (($percentCover =~ m/%/) || ($percentCover !~ m#n/a#)) {
     $customKey = $percentCover;
     $customKey =~ s/[ %]+//;
   }
   return ($itemCount, $percentCover, $customKey);
 }	#	sub computeTrackCell($$$$)
 
 # render one <td> cell from a (itemCount, percentCover, customKey) triple
 sub renderCell($$$) {
   my ($itemCount, $percentCover, $customKey) = @_;
   if (length($customKey)) {
     return sprintf("    <td style='text-align: right;' sorttable_customkey='%s'>%s<br>(%s)</td>\n", $customKey, $itemCount, $percentCover);
   } elsif ($itemCount eq "n/a") {
     return "    <td style='text-align: right;'>n/a</td>\n";
   } else {
     return sprintf("    <td style='text-align: right;'>%s<br>(%s)</td>\n", $itemCount, $percentCover);
   }
 }
 
 ##############################################################################
 ### tableContentsBoth()
 ### walks @orderList exactly once, measuring each assembly's tracks exactly
 ### once, and returns the table body HTML for both the production and
 ### -test pages (plus each page's column count, for endTable()'s colspan).
 ##############################################################################
 sub tableContentsBoth() {
   my @prodTrackList = buildTrackList(0, $asmHubName);
   my @testTrackList = buildTrackList(1, $asmHubName);
   my %inUnion;
   my @unionTracks = grep { !$inUnion{$_}++ } (@prodTrackList, @testTrackList);
 
   my $prodBody = "";
   my $testBody = "";
   my $asmCounted = 0;
 
   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}/${asmId}.faSize.txt";
     }
     if (! -s "$asmReport") {
       printf STDERR "# no assembly report:\n# %s\n", $asmReport;
       next;
     }
     if (! -s "$twoBit") {
       printf STDERR "# no 2bit file:\n# %s\n", $twoBit;
       my $missingRow = sprintf("<tr><td style='text-align: right;'>%d</td>\n", ++$asmCount);
       $missingRow .= sprintf("<td style='text-align: center;'>%s</td>\n", $accessionId);
       $missingRow .= "<th colspan=15 style='text-align: center;'>missing masked 2bit file</th>\n";
       $missingRow .= "</tr>\n";
       $prodBody .= $missingRow;
       $testBody .= $missingRow;
       next;
     }
     if ( ! -s "$faSizeTxt" ) {
        printf STDERR "faSize $twoBit > $faSizeTxt\n";
        print `faSize $twoBit > $faSizeTxt`;
     }
     my ($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";
     $sciName = $sciNameOverride{$accessionId} if (defined($sciNameOverride{$accessionId}));
     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/\r//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);
 
     # the browser/hub links are the only thing that differ between the
     # two pages besides the columns themselves
     my $browserName = $commonName;
     my $prodBrowserUrl = "https://genome.ucsc.edu/h/$accessionId";
     my $testBrowserUrl = "https://genome-test.gi.ucsc.edu/h/$accessionId";
     if ($asmId !~ m/^GC/) {
        $prodBrowserUrl = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=$asmId";
        $testBrowserUrl = "https://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=$asmId";
        $browserName = "$commonName ($asmId)";
     }
 
     ++$asmCount;
     my $prodRow = sprintf("<tr><td style='text-align: right;'>%d</td>\n", $asmCount);
     $prodRow .= sprintf("<td style='text-align: center;'><a href='%s' target=_blank>%s<br>%s</a></td>\n", $prodBrowserUrl, $browserName, $accessionId);
     my $testRow = sprintf("<tr><td style='text-align: right;'>%d</td>\n", $asmCount);
     $testRow .= sprintf("<td style='text-align: center;'><a href='%s' target=_blank>%s<br>%s</a></td>\n", $testBrowserUrl, $browserName, $accessionId);
 
     # measure every track needed by either page exactly once
     my %cell;	# key is track name, value is [itemCount, percentCover, customKey]
     foreach my $track (@unionTracks) {
       $cell{$track} = [ computeTrackCell($asmId, $track, $buildDir, $totalSize) ];
     }
 
     foreach my $track (@prodTrackList) {
       my ($itemCount, $percentCover, $customKey) = @{$cell{$track}};
       $tracksCounted += 1 if ($itemCount ne "n/a");
       $prodRow .= renderCell($itemCount, $percentCover, $customKey);
     }
     foreach my $track (@testTrackList) {
       my ($itemCount, $percentCover, $customKey) = @{$cell{$track}};
       $testRow .= renderCell($itemCount, $percentCover, $customKey);
     }
     $prodRow .= "</tr>\n";
     $testRow .= "</tr>\n";
     $prodBody .= $prodRow;
     $testBody .= $testRow;
 
     $asmCounted += 1;
     if ($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, $asmId;
     }
   }
   return ($prodBody, $testBody, scalar(@prodTrackList), scalar(@testTrackList));
 }	#	sub tableContentsBoth()
 
 ##############################################################################
 ### 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);
 
 my $header = capture { startHtml() };
 my ($prodBody, $testBody, $prodCols, $testCols) = tableContentsBoth();
 my $prodHead = capture { startTable(0) };
 my $testHead = capture { startTable(1) };
 my $prodFoot = capture { endTable($assemblyTotal, $asmCount, $prodCols) };
 my $testFoot = capture { endTable($assemblyTotal, $asmCount, $testCols) };
 my $footer = capture { endHtml() };
 
 open(my $pfh, '>', $prodOutFile) or die "can not write $prodOutFile";
 print $pfh $header, $prodHead, $prodBody, $prodFoot, $footer;
 close($pfh);
 
 open(my $tfh, '>', $testOutFile) or die "can not write $testOutFile";
 print $tfh $header, $testHead, $testBody, $testFoot, $footer;
 close($tfh);