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/jaxQtlMapped.html src/hg/makeDb/trackDb/jaxQtlMapped.html
index b1790b7..beff67b 100644
--- src/hg/makeDb/trackDb/jaxQtlMapped.html
+++ src/hg/makeDb/trackDb/jaxQtlMapped.html
@@ -1,19 +1,19 @@
 <H2>Description</H2>
 <P>
 This track shows Mouse quantitative trait loci (QTLs) from 
-<A HREF="http://www.informatics.jax.org/" 
+<A HREF="https://www.informatics.jax.org//" 
 TARGET=_BLANK>Mouse Genome Informatics</A> (MGI) at the 
 <A HREF="https://www.jax.org/" TARGET=_BLANK>Jackson Laboratory</A> 
 that have been coarsely mapped by UCSC to the $Organism genome using 
 stringently filtered cross-species alignments.  
 A quantitative trait locus (QTL) is a polymorphic locus that contains alleles
 which differentially affect the expression of a continuously distributed 
 phenotypic trait. Usually a QTL is a marker described by statistical 
 association to quantitative variation in the particular phenotypic trait that
 is thought to be controlled by the cumulative action of alleles at multiple 
 loci.</P>
 <P>
 To map the Mouse QTLs to $Organism, UCSC's chained and netted blastz
 alignments of Mouse to $Organism were filtered to retain only those with
 minimum length of 20,000 bases in both Mouse and $Organism, and minimum 
 score of 10,000.  This removed many valid-but-short alignments.  This
@@ -33,19 +33,19 @@
 conservative proxy for the unknown confidence interval.  The two 
 categories of QTL are displayed in subtracks: MGI Mouse QTL for the 
 unmodified QTLs and MGI Mouse QTL Padded for the single-marker QTLs 
 that were padded to 100,000 bases.
 </P>
 <P>
 To get a sense of how many genomic rearrangments between Mouse and
 $Organism are in the region of a particular Mouse QTL, you may want to
 view the $Organism Nets track in the Mouse $o_date genome browser.  
 In the position/search box, enter the name of the Mouse QTL of interest.
 </P>
 
 <H2>Credits</H2>
 <P>
 Thanks to 
-<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A> 
+<A HREF="https://www.informatics.jax.org//" TARGET=_BLANK>MGI</A> 
 at the Jackson Laboratory, 
 and Bob Sinclair in particular, for providing these data.</P>
 </P>