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
@@ -37,30 +37,32 @@
}
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
@@ -155,44 +157,65 @@
VGP - Vertebrate Genomes Project assembly hubs, track statistics
This assembly hub contains assemblies released
by the
Vertebrate Genomes Project. $vgpSubset
END
} else {
+ if ($hprcIndex) {
+ print <<"END"
+
+
+
+
+
+
+HPRC - Human Pangenome Reference Consortium assembly hubs, track statistics
+
+
+
+
+This assembly hub contains assemblies released
+by the
+Human Pangenome Reference Consortium.
+
+
+END
+ } else {
print <<"END"
$Name Genomes assembly hubs, track statistics
Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
END
}
+}
my $indexUrl = "index";
my $asmStats = "asmStats";
print <<"END"
Data resource links
NOTE: Click on the column headers to sort the table by that column
The link to genome browser will attach only that single assembly to
the genome browser.
The numbers are: item count (percent coverage)
Except for the gc5Base column which is: overall GC % average (percent coverage)
END
} # sub startHtml()
# order of columns in the table