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/commonHtml.pm src/hg/makeDb/doc/asmHubs/commonHtml.pm
index 6be84f6..2f3e2fe 100644
--- src/hg/makeDb/doc/asmHubs/commonHtml.pm
+++ src/hg/makeDb/doc/asmHubs/commonHtml.pm
@@ -1,122 +1,132 @@
 package commonHtml;
 
 # helper functions for common HTML output features
 
 use warnings;
 use strict;
 use Carp;
 use vars qw(@ISA @EXPORT_OK);
 use Exporter;
 
 @ISA = qw(Exporter);
 
 # This is a listing of the public methods and variables (which should be
 # treated as constants) exported by this module:
 @EXPORT_OK = (
   qw( otherHubLinks htmlFooter )
 );
 
 # otherHubLinks: arg one: vgpIndex, arg two: asmHubName, arg three: orderList
 # arguments allow decision on customization of the table for different
 # types of assembly hubs
 
 sub otherHubLinks($$) {
 
   my ($vgpIndex, $asmHubName) = @_;
 
 my %asmCounts;	# key is hubName, value is number of assemblies
-my @hubList = qw(primates mammals birds fish vertebrate invertebrate plants fungi viral);
+my @hubList = qw(primates mammals birds fish vertebrate invertebrate plants fungi viral bacteria);
 foreach my $hubName (@hubList) {
   my $asmCount = `grep -v "^#" ../${hubName}AsmHub/${hubName}.orderList.tsv | wc -l`;
   chomp $asmCount;
   $asmCounts{$hubName} = $asmCount;
 }
 my $vgpCount = `grep -h -v "^#" ../vgpAsmHub/vgp.*.orderList.tsv | wc -l`;
 chomp $vgpCount;
 $asmCounts{'vgp'} = $vgpCount;
-my $legacyCount = `grep -h -v "^#" ../legacyAsmHub/legacy.orderList.tsv | wc -l`;
+my $hprcCount = `grep -c -h -v "^#" ../hprcAsmHub/hprc.orderList.tsv`;
+chomp $hprcCount;
+$asmCounts{'hprc'} = $hprcCount;
+my $legacyCount = `grep -c -h -v "^#" ../legacyAsmHub/legacy.orderList.tsv`;
 chomp $legacyCount;
 $asmCounts{'legacy'} = $legacyCount;
 
 # different table output for VGP index
 
 if ((0 == $vgpIndex)) {
   printf "<p>\n<table border='1' style='margin-left:auto; margin-right:auto;'><thead>\n";
   printf "<tr><th colspan=4 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n";
   printf "<tr><th>Collection</th>\n";
   printf "    <th>Hub index pages:</th>\n";
   printf "    <th>Assembly statistics:</th>\n";
   printf "    <th>Track statistics:</th>\n";
   printf "</tr>\n";
   foreach my $hubName (@hubList) {
     if ($hubName =~ m/^vertebrate/) {
       printf "<tr><th>other vertebrates</th>\n";
     } elsif ($hubName =~ m/fish/) {
       printf "<tr><th>Fishes</th>\n";
     } elsif ($hubName =~ m/invertebrate/) {
       printf "<tr><th>Invertebrates</th>\n";
     } elsif ($hubName =~ m/viral/) {
       printf "<tr><th>Viruses</th>\n";
+    } elsif ($hubName =~ m/bacteria/) {
+      printf "<tr><th>Bacteria</th>\n";
     } else {
       printf "<tr><th>%s</th>\n", ucfirst($hubName);
     }
     printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", $hubName, $asmCounts{$hubName};
     printf "    <th><a href='../%s/asmStats.html'>assembly stats</a></th>\n", $hubName;
     printf "    <th><a href='../%s/trackData.html'>track stats</a></th>\n", $hubName;
     printf "</tr>\n";
   }
   printf "<tr><th>VGP - Vertebrate Genome Project</th>\n";
   printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "VGP", $asmCounts{'vgp'};
   printf "    <th><a href='../VGP/asmStats.html'>assembly stats</a></th>\n";
   printf "    <th><a href='../VGP/trackData.html'>track stats</a></th>\n";
   printf "</tr>\n";
+  printf "<tr><th>HPRC - Human Pangenome Reference Consortium</th>\n";
+  printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "HPRC", $asmCounts{'hprc'};
+  printf "    <th><a href='../HPRC/asmStats.html'>assembly stats</a></th>\n";
+  printf "    <th><a href='../HPRC/trackData.html'>track stats</a></th>\n";
+  printf "</tr>\n";
   printf "<tr><th>legacy/superseded</th>\n";
   printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "legacy", $asmCounts{'legacy'};
   printf "    <th><a href='../legacy/asmStats.html'>assembly stats</a></th>\n";
   printf "    <th><a href='../legacy/trackData.html'>track stats</a></th>\n";
   printf "</tr></thead>\n</table>\n</p>\n";
 } elsif (1 == $vgpIndex) {
   printf "<p>\n<table border='1'><thead>\n";
   printf "<tr><th colspan=5 style='text-align:center;'>Alternate sets of VGP assemblies</th><th style='text-align:center;'>NCBI Refseq</th></tr>\n";
   printf "<tr><th>Index pages:&nbsp;</th>\n";
   printf "<th><a href='index.html'>primary assembly</a></th>\n";
   printf "<th><a href='vgpAlt.html'>alternate/haplotype</a></th>\n";
   printf "<th><a href='vgpTrio.html'>trio mat/pat</a></th>\n";
   printf "<th><a href='vgpLegacy.html'>legacy/superseded</a></th>\n";
   printf "<th><a href='../primates/index.html'>other NCBI Refseq assemblies</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "<th>Assembly statistics:&nbsp;</th>\n";
   printf "<th><a href='asmStats.html'>primary assembly</a></th>\n";
   printf "<th><a href='vgpAltStats.html'>alternate/haplotype</a></th>\n";
   printf "<th><a href='vgpTrioStats.html'>trio mat/pat</a></th>\n";
   printf "<th><a href='vgpLegacyStats.html'>legacy/superseded</a></th>\n";
   printf "<th><a href='../primates/asmStats.html'>other NCBI Refseq assemblies</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "<th>Track statistics:&nbsp;</th>\n";
   printf "<th><a href='trackData.html'>primary assembly</a></th>\n";
   printf "<th><a href='vgpAltData.html'>alternate/haplotype</a></th>\n";
   printf "<th><a href='vgpTrioData.html'>trio mat/pat</a></th>\n";
   printf "<th><a href='vgpLegacyData.html'>legacy/superseded</a></th>\n";
   printf "<th><a href='../primates/trackData.html'>other NCBI Refseq assemblies</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "</tr></thead>\n</table>\n</p>\n";
 }
 
 }	#	sub otherHubLinks($$)
 
 ############################################################################
 # common output at the bottom of an html index page
 sub htmlFooter() {
 
 print <<"END"
 </div><!-- closing gbsPage from gbPageStartHardcoded.html -->
 </div><!-- closing container-fluid from gbPageStartHardcoded.html -->
 <!--#include virtual="\$ROOT/inc/gbFooterHardcoded.html"-->
 <script type="text/javascript" src="<!--#echo var="ROOT" -->/js/sorttable.js"></script>
 </body></html>
 END
 }
 ############################################################################