2e3c89f43f3bb9d386178270200d0acce9fc8050
lrnassar
  Fri Nov 22 17:47:13 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.

diff --git src/hg/makeDb/trackDb/human/snpRecombRate.html src/hg/makeDb/trackDb/human/snpRecombRate.html
index 02c2870..76da881 100644
--- src/hg/makeDb/trackDb/human/snpRecombRate.html
+++ src/hg/makeDb/trackDb/human/snpRecombRate.html
@@ -36,31 +36,31 @@
 <H2>Methods</H2>
 <P>
 Fine-scale recombination rates are estimated using the reversible-jump
 Markov chain Monte Carlo (MCMC) method (McVean <em>et al</em>., 2004).  This
 approach explores the posterior distribution of fine-scale recombination
 rate profiles, where the state-space considered is the distribution of
 piece-wise constant recombination maps.  The Markov chain explores the
 distribution of both the number and location of change-points, in addition
 to the rates for each segment.  A prior is set on the number of
 change-points that increases the smoothing effect of trans-dimensional
 MCMC, which is necessary because of the composite-likelihood scheme
 employed.
 </P>
 <P>
 This method is implemented in the package 
-<A HREF="http://www.stats.ox.ac.uk/~mcvean/LDhat/" TARGET=_blank>LDhat</A>, 
+<A HREF="https://www.stats.ox.ac.uk/~mcvean/LDhat/" TARGET=_blank>LDhat</A>, 
 which includes full details of installation and implementation.
 </P>
 <P>
 A block-penalty of five was used (calibrated by simulation 
 and comparison to data from sperm-typing studies).  Each region was
 analyzed as a single run with 10,000,000 iterations, sampling every 5000th
 iteration and discarding the first third of all samples as burn-in.  The
 mean posterior rate for each SNP interval is the value reported.  Because of 
 the non-independence of the composite likelihood scheme,
 the quantiles of the sampling distribution do not reflect true uncertainty
 and are therefore not given.
 </P>
 <P>
 Estimates were generated separately from each of the four HapMap 
 populations, and then combined to give a single figure.  Differences between 
@@ -69,31 +69,31 @@
 
 <H2>Validation</H2>
 <P>
 This approach has been validated in three ways: by extensive
 simulation studies and by comparisons with independent estimates of
 recombination rates, both over large scales from the genetic map and
 over fine scales from sperm analysis.  Full details of validation can be 
 found in McVean <em>et al</em>. (2004) and Winckler <em>et al</em>. (2005).
 </P>
 
 <H2>Credits</H2>
 <P>
 The HapMap data are based on <A HREF="https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/" TARGET=_blank>HapMap</A> 
 release 16a; the Perlegen data are from Hinds <em>et al</em>. (2005).  
 The recombination rates were ascertained by Simon Myers from the
-<A HREF="http://mathgen.stats.ox.ac.uk/"
+<A HREF="https://mathgen.stats.ox.ac.uk/"
 TARGET=_blank>Mathematical Genetics Group</A> at the University of Oxford.
 </P>
 
 <H2>References</H2>
 <P>
 Crawford, D.C., Bhangale, T., Li, N., Hellenthal, G., Rieder, M.J., 
 Nickerson, D.A. and Stephens, M.
 <A HREF="https://www.nature.com/articles/ng1376"
 TARGET=_blank>Evidence for substantial fine-scale variation in recombination 
 rates across the human genome</A>.
 <em>Nat Genet.</em> <B>36</B>(7), 700-6 (2004).
 </P>
 <P>
 Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J. and  Lander, E.S.
 <A HREF="https://www.nature.com/articles/ng1001-229"