1682366b1827b7559f8e1e41635acff6c5ea15e9
max
  Wed Sep 9 06:05:05 2026 -0700
hprc2annot: move the makeDoc into its own directory and repoint the links

The makeDoc has grown a companion (an hg38 pcLAI doc is in progress), so it
moves from doc/contrib/hprc2annot.txt into doc/contrib/hprc2annot/, matching
how the scripts and trackDb copies are already laid out. The file itself gains
a section on the pcLAI scatterplot on the details page: where the reference
panel comes from, the four ancestry centroids the discretized field takes
across the release, and why the file is read through hgTrackUi rather than
fetched by the browser.

All seven track description pages linked to the old flat path and would have
404'd, so they are repointed. Six of them change only that link; pclai.html has
further edits still in progress and keeps its own copy of the change.

refs #35415

diff --git src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html
index 599bff30b54..28576c83e7e 100644
--- src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html
@@ -23,31 +23,31 @@
 
 <h2>Methods</h2>
 <p>
 The cenSat annotation identifies and classifies satellite arrays in a complete
 assembly, combining alpha-satellite higher-order-repeat detection with a
 repeat-family classification of the remaining satellite sequence, following the
 approach developed for the telomere-to-telomere CHM13 reference (see reference
 below).
 </p>
 <p>
 The annotation files were obtained from the HPRC Release 2 data collection on the
 public <tt>s3://human-pangenomics</tt> bucket, indexed at
 <a href="https://github.com/human-pangenomics/hprc_intermediate_assembly/tree/main/data_tables/annotation/censat" target="_blank">the hprc_intermediate_assembly data tables</a>.
 Each per-assembly cenSat BED file was converted to a UCSC bigBed file, preserving
 the item colors. The steps are described in the
-<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/contrib/hprc2annot.txt" target="_blank">makeDoc</a>,
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/contrib/hprc2annot/hprc2annot.txt" target="_blank">makeDoc</a>,
 the build scripts are in the
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/hprc2annot" target="_blank">kent source tree</a>,
 and the track configuration is in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/trackDb/contrib/hprc2annot" target="_blank">trackDb/contrib/hprc2annot</a>.
 </p>
 
 <h2>Data Access</h2>
 <p>
 For automated analysis, the annotation is stored in a bigBed-format file
 (<tt>censat.bb</tt>) that can be read with the UCSC tool <tt>bigBedToBed</tt>,
 which can be compiled from source or downloaded as a precompiled binary. The
 original annotation files are available from the HPRC S3 bucket linked above.
 </p>
 
 <h2>Credits</h2>