8c2f7318d8d821de9b2a25750586a94ab5e8c1bb
lrnassar
  Fri Nov 15 18:50:19 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/nestedRepeatsRM327.html src/hg/makeDb/trackDb/nestedRepeatsRM327.html
index d27d2a2..2c5b188 100644
--- src/hg/makeDb/trackDb/nestedRepeatsRM327.html
+++ src/hg/makeDb/trackDb/nestedRepeatsRM327.html
@@ -1,86 +1,86 @@
 <H2>Description</H2>
 <P>
 This track shows joined fragments of interrupted repeats extracted from 
 the output of a more recent version (3.2.7, Jan. 2009) of the
-<A HREF="http://www.repeatmasker.org/"
+<A HREF="https://www.repeatmasker.org/"
 TARGET=_blank>RepeatMasker</A> program, which screens DNA sequences 
 for interspersed repeats and low complexity DNA sequences using 
 the <A HREF="https://www.girinst.org/repbase/update/index.html"
 TARGET=_blank>Repbase Update</A> library of repeats from the 
 <A HREF="https://www.girinst.org/" TARGET=_blank>Genetic 
 Information Research Institute</A> (GIRI).  
 Repbase Update is described in Jurka, J. (2000) in the References section below.
 </P>
 <P>
 The detailed annotations from RepeatMasker are in the RepMask 3.2.7
 track.  This track shows fragments of original repeat insertions 
 which have been
 interrupted by insertions of younger repeats or through local
 rearrangements.  The fragments are joined using the ID column of
 RepeatMasker output.
 </P>
 <P>
 Interrupted repeats from the original RepeatMasker run have been kept in the
 Interrupted Rpts track in order to avoid disrupting any analyses performed
 on the original run's results.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 In pack or full mode, each interrupted repeat is displayed as boxes
 (fragments) joined by horizontal lines, labeled with the repeat name.
 If all fragments are on the same strand, then arrows are added to the
 horizontal line to indicate strand.  In dense or squish mode, labels 
 and arrows are omitted, and in dense mode, all items are collapsed to 
 fit on a single row.
 </P>
 <P>
 Items are shaded according to the average identity score of their
 fragments.  Usually, the shade of an item is similar to the shades of
 its fragments, unless some fragments are much more diverged than
 others.  The score displayed above is the average identity score,
 clipped to a range of 50% - 100%, and then mapped to the range
 0 - 1000 for shading in the browser.
 </P>
 
 <H2>Methods</H2>
 <P>
 UCSC has used the most current versions of the RepeatMasker software 
 and repeat libraries available to generate these data. Note that these 
 versions may be newer than those that are publicly available on the Internet. 
 </P>
 <P>
 Data are generated using the RepeatMasker <em>-s</em> flag. Additional flags
 may be used for certain organisms.  See the 
 <A HREF="../FAQ/FAQdownloads#download16">FAQ</A> for 
 more information. </P>
 
 <H2>Credits</H2>
 <P>
 Thanks to Arian Smit, Robert Hubley and GIRI
 for providing the tools and repeat libraries used to generate this track.</P>
 
 <H2>References</H2>
 <P>
 Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.
-<A HREF="http://www.repeatmasker.org" 
-TARGET=_BLANK>http://www.repeatmasker.org</A>. 1996-2007.
+<A HREF="https://www.repeatmasker.org/" 
+TARGET=_BLANK>https://www.repeatmasker.org/</A>. 1996-2007.
 </P>
 <P>
 Repbase Update is described in 
 Jurka J. 
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10973072"
 TARGET=_blank>Repbase update: a database and an electronic journal of 
 repetitive elements</A>. 
 <em>Trends Genet</em>. 2000 Sep;16(9):418-420.</P>
 <P>
 For a discussion of repeats in mammalian genomes, see: 
 <P>
 Smit AF. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10607616"
 TARGET=_blank>Interspersed repeats and other mementos of transposable 
 elements in mammalian genomes</A>. <em>Curr Opin Genet Dev</em>. 1999 Dec;9(6):
 657-63.</P>
 <P>
 Smit AF. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8994846"
 TARGET=_blank>The origin of interspersed repeats in the human genome</A>. 
 <em>Curr Opin Genet Dev</em>. 1996 Dec;6(6):743-8.
 </P>