089c09e98db52e92da694ab1a0c8891c1a7fd3e8
gperez2
  Thu Apr 2 15:50:07 2026 -0700
Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run).

Updated 261 trackDb HTML and .ra files:
- Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs,
chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations;
removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download,
oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs).
- Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com,
drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains
(blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix);
removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com).
- Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org,
cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org,
hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path).

No RM.

diff --git src/hg/makeDb/trackDb/human/snpMap.html src/hg/makeDb/trackDb/human/snpMap.html
index 84614ead72c..210db079e4f 100644
--- src/hg/makeDb/trackDb/human/snpMap.html
+++ src/hg/makeDb/trackDb/human/snpMap.html
@@ -104,37 +104,37 @@
 Consortium</A> and <A HREF="https://www.ncbi.nlm.nih.gov"
 TARGET=_blank>NIH</A> for providing the public data, which are available from 
 <A HREF="https://www.ncbi.nlm.nih.gov/SNP" TARGET=_blank>dbSnp</A> at 
 NCBI.</P>
 <P>
 Thanks to <A HREF="http://www.perlegen.com" TARGET=_blank>Perlegen Sciences, 
 Inc.</A> for providing additional SNPs from their database.
 Additional information about the Perlegen SNP discovery process can be
 found in Patil, N. (2001) 
 <A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5547/1719"
 TARGET=_blank> 
 Blocks of Limited Haplotype Diversity Revealed by High-Resolution
 Scanning of Human Chromosome 21</A>. <i>Science</i> 294:1719-1723.
 </p>
 <P>
-Thanks to <A HREF="http://www.affymetrix.com"
+Thanks to <A HREF="https://www.affymetrix.com"
 TARGET=_blank>Affymetrix, Inc.</A> for developing the genotyping
 arrays. For more details on this genotyping assay, please see the
 supplemental information on the 
-<A HREF="http://www.affymetrix.com/support/technical/byproduct.affx?product=10k" 
+<A HREF="https://www.affymetrix.com/support/technical/byproduct.affx?product=10k" 
 TARGET=_blank>Affymetrix 10K SNP</A> and 
-<A HREF="http://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx" 
+<A HREF="https://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx" 
 TARGET=_blank>Affymetrix 120K SNP</A> products. Additional information, 
 including genotyping data, is available from the details pages for the 
 Affymetrix 120K SNP and Affymetrix 10K SNP tracks.</P>
 
 <H2>Terms of Use for the Affymetrix data</H2>
 <P> Please see the <A HREF="https://www.affymetrix.com:443/site/terms.affx"
 TARGET=_blank>Terms and Conditions</A> page on the Affymetrix website for 
 restrictions on the use of their data. 
 
 <!--
 <P>During sample preparation, an <B>enzyme</B> is used to fragment the
 genomic DNA into smaller pieces.  The restriction endonucleases
 <I><B>HindIII</B></I> and <I><B>XbaI</B></I> have been used to generate this
 data.</P>