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
@@ -39,31 +39,31 @@
 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