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/apis/rmsk.html src/hg/makeDb/trackDb/apis/rmsk.html
index 718611e..b9a51ea 100644
--- src/hg/makeDb/trackDb/apis/rmsk.html
+++ src/hg/makeDb/trackDb/apis/rmsk.html
@@ -1,65 +1,65 @@
 <H2>Description</H2>
 <P>
 This track was created by using Arian Smit's <A
-HREF="http://www.repeatmasker.org/"
+HREF="https://www.repeatmasker.org/"
 TARGET=_blank>RepeatMasker</A> program, which screens DNA sequences 
 for interspersed repeats and low complexity DNA sequences. The program
 outputs a detailed annotation of the repeats that are present in the
 query sequence (represented by this track), as well as a modified version
 of the query sequence in which all the annotated repeats have been masked
 (generally available on the
 <A HREF="http://hgdownload.soe.ucsc.edu/downloads.html"
 TARGET=_BLANK>Downloads</A> page). RepeatMasker uses 
 the <A HREF="https://www.girinst.org/repbase/update/"
 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>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 In full display mode, this track displays up to ten different classes of repeats:
 <UL>
 <LI>Short interspersed nuclear elements (SINE), which include ALUs
 <LI>Long interspersed nuclear elements (LINE)
 <LI>Long terminal repeat elements (LTR), which include retroposons
 <LI>DNA repeat elements (DNA)
 <LI>Simple repeats (micro-satellites)
 <LI>Low complexity repeats
 <LI>Satellite repeats
 <LI>RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA)
 <LI>Other repeats, which includes class RC (Rolling Circle)
 <LI>Unknown
 </UL></P>
 <P>
 The level of color shading in the graphical display reflects the amount of 
 base mismatch, base deletion, and base insertion associated with a repeat 
 element. The higher the combined number of these, the lighter the shading.</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.  Repeats are soft-masked. Alignments may 
 extend through repeats, but are not permitted to initiate in them. 
 See the 
 <A HREF="../FAQ/FAQdownloads#download16">FAQ</A> for 
 more information. </P>
 
 <H2>Credits</H2>
 <P>
 Thanks to Arian Smit and GIRI
 for providing the tools and repeat libraries used to generate this track.</P>
 
 <H2>References</H2>
 <p>
 Jurka J.
 <a href="https://www.sciencedirect.com/science/article/pii/S016895250002093X"
 target="_blank">Repbase update: a database and an electronic journal of repetitive elements</a>.
 <em>Trends Genet</em>. 2000 Sep;16(9):418-20.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10973072" target="_blank">10973072</a>
 </p>