src/hg/makeDb/doc/asmHubs/mkAsmStats.pl 790b166f17ba0ef2f8cfe220dbc6c2a67035ede9

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/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
index 03ed644..788338c 100755
--- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
+++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
@@ -22,30 +22,32 @@
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 
 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
 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
@@ -80,44 +82,65 @@
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>VGP - Vertebrate Genomes Project assembly hubs, assembly 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 ($hprcIndex) {
+    print <<"END"
+<!DOCTYPE HTML 4.01 Transitional>
+<!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium assembly hubs, assembly statistics" -->
+<!--#set var="ROOT" value="../.." -->
+
+<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
+
+<h1>VGP - Human Pangenome Reference Consortium assembly hubs, assembly statistics</h1>
+<p>
+<a href='https://humanpangenome.org/' target=_blank>
+<img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p>
+<p>
+This assembly hub contains assemblies released
+by the <a href='https://humanpangenome.org/' target=_blank>
+Human Pangenome Reference Consortium.</a>
+</p>
+
+END
+  } else {
     print <<"END"
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="$Name genomes assembly hubs, assembly statistics" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>$Name Genomes assembly hubs, assembly statistics</h1>
 <p>
 Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
 </p>
 
 END
   }
+}
 
   print <<"END"
 <h3>See also: <a href='index.html'>hub access</a>,&nbsp;<a href='trackData.html'>track 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.
 END
 }
 
 ##############################################################################
 ### start the table output
 ##############################################################################
 sub startTable() {