27a61987f2692b2fad37a9faada47b927f568e1e
hiram
  Fri May 24 10:11:44 2024 -0700
correct ftp to https for references to ftp.ncbi.nih.gov no redmine

diff --git src/hg/utils/automation/asmHubWindowMasker.pl src/hg/utils/automation/asmHubWindowMasker.pl
index 8202415..e779b2e 100755
--- src/hg/utils/automation/asmHubWindowMasker.pl
+++ src/hg/utils/automation/asmHubWindowMasker.pl
@@ -1,86 +1,86 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 3) {
   printf STDERR "usage: asmHubWindowMasker.pl asmId asmId.names.tab buildDir\n";
   printf STDERR "where asmId is the assembly identifier,\n";
   printf STDERR "and   asmId.names.tab is naming file for this assembly,\n";
   printf STDERR "and   buildDir is the directory with bbi/asmId.windowMasker.bb\n";
   exit 255;
 }
 
 my $asmId = shift;
 my $namesFile = shift;
 my $buildDir = shift;
 my $wmBbi = "$buildDir/bbi/$asmId.windowMasker.bb";
 my $chromSizes = "$buildDir/$asmId.chrom.sizes";
 
 if ( ! -s $wmBbi ) {
   printf STDERR "ERROR: can not find windowMasker bbi file:\n\t'%s'\n", $wmBbi;
   exit 255;
 }
 
 my $em = "<em>";
 my $noEm = "</em>";
 my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`;
 chomp $assemblyDate;
 my $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`;
 chomp $ncbiAssemblyId;
 my $organism = `grep -v "^#" $namesFile | cut -f5`;
 chomp $organism;
 my $basesCovered = `bigBedInfo $wmBbi | egrep "basesCovered:" | sed -e 's/basesCovered: //;'`;
 chomp $basesCovered;
 my $bases = $basesCovered;
 $bases =~ s/,//g;
 my $asmSize = &AsmHub::asmSize($chromSizes);
 my $percentCoverage = sprintf("%.2f", (100.0 * $bases) / $asmSize);
 $asmSize = &AsmHub::commify($asmSize);
 
 print <<_EOF_
 <h2>Description</h2>
 <p>
 This track depicts masked sequence as determined by <a href="
 http://bioinformatics.oxfordjournals.org/content/22/2/134.full" target="_blank">WindowMasker</a> on the
 the $assemblyDate $em${organism}$noEm/$asmId/$ncbiAssemblyId genome assembly.
 The WindowMasker tool is included in the NCBI C++ toolkit. The source code
 for the entire toolkit is available from the NCBI
-<a href="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/" target="_blank">
+<a href="https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/" target="_blank">
 FTP site</a>.
 </p>
 
 <h2>Methods</h2>
 <p>
 To create this track, WindowMasker was run with the following parameters:
 <pre>
 windowmasker -mk_counts true -input $asmId.unmasked.fa -output wm_counts
 windowmasker -ustat wm_counts -sdust true -input $asmId.unmasked.fa -output windowmasker.intervals
 perl -wpe 'if (s/^&gt;lcl\\|(.*)\\n&dollar;//) { &dollar;chr = &dollar;1; } \\
    if (/^(\\d+) - (\\d+)/) { \\
    &dollar;s=&dollar;1; &dollar;e=&dollar;2+1; s/(\\d+) - (\\d+)/&dollar;chr\\t&dollar;s\\t&dollar;e/; \
    }' windowmasker.intervals &gt; windowmasker.sdust.bed
 </pre>
 The windowmasker.sdust.bed included masking for areas of the
 assembly that are gap.  The file was 'cleaned' to remove those areas
 of masking in gaps, leaving only the sequence masking.  The final
 result covers $basesCovered bases in the assembly size $asmSize for
 a percent coverage of % $percentCoverage.
 </p>
 
 <h2>References</h2>
 
 <p>
 Morgulis A, Gertz EM, Sch&auml;ffer AA, Agarwala R.
 <a href="http://bioinformatics.oxfordjournals.org/content/22/2/134.full" target="_blank">
 WindowMasker: window-based masker for sequenced genomes</a>.
 <em>Bioinformatics</em>. 2006 Jan 15;22(2):134-41.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16287941" target="_blank">16287941</a>
 </p>
 _EOF_
    ;