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/affy10K.html src/hg/makeDb/trackDb/human/affy10K.html
index f82509df50d..7861ab996ae 100644
--- src/hg/makeDb/trackDb/human/affy10K.html
+++ src/hg/makeDb/trackDb/human/affy10K.html
@@ -1,51 +1,51 @@
 <H2>Description</H2>
 
 <P>This track shows locations of the Single Nucleotide Polymorphisms
 on the Affymetrix 10K Mapping Array.  The SNPs in this track include
 all of the markers from the array that have been successfully mapped
 against the current assembly.</P>
 
 <P>The SNPs were selected from public domain databases. Genotypes for
 these markers were generated at Affymetrix using GeneChip(r) DNA
 analysis technology and are available at their site.</P>
 
 <!--
 <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>
 
 <P>Genotypes are reported as pairs of basecalls representing the two
 observed alleles.  Individual genotypes for which no call was made are
 labeled 'NC'.  A minimum of 46 genotype calls in the set of 54
 individuals are included for each SNP.</P>
 
 <P><B>Allele Frequency</B> for the 'A' allele is two times the number
 of 'AA' calls plus the number of 'AB' calls, divided by two times the
 total number of calls.  Allele Frequency for the 'B' allele is two
 times the number of 'BB' calls plus the number of 'AB' calls, divided
 by two times the total number of calls.  The <B>Minimum Allele
 Frequency</B> is the lesser of these two values.
 <B>Heterozygosity</B> is two times the product of the two allele
 frequencies.</P> 
 -->
 
 <H2>Credits</H2>
 
 <P>Thanks to <A HREF="https://www.ncbi.nlm.nih.gov/SNP"
 TARGET=_blank>dbSnp</A> at the NCBI for providing the public SNPs.
 
-<P>Thanks to <A HREF="http://www.affymetrix.com"
+<P>Thanks to <A HREF="https://www.affymetrix.com"
 TARGET=_blank>Affymetrix, Inc.</A> for developing the genotyping
 array.  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"
+HREF="https://www.affymetrix.com/support/technical/byproduct.affx?product=10k"
 TARGET=_blank>Affymetrix 10K SNP</A> product.</P>
 
 <H2>Terms of Use</H2>
 <P>Please see the <A HREF="https://www.affymetrix.com:443/site/terms.affx"
 TARGET=_blank>Terms and Conditions</A> for the use of this data at the
-<A HREF="http://www.affymetrix.com" TARGET=_blank>Affymetrix, Inc.</A>
+<A HREF="https://www.affymetrix.com" TARGET=_blank>Affymetrix, Inc.</A>
 site.</P>