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/censatCentromeres.html src/hg/makeDb/trackDb/contrib/hprc2annot/censatCentromeres.html
index dd1c271870b..17ab1c8e4e4 100644
--- src/hg/makeDb/trackDb/contrib/hprc2annot/censatCentromeres.html
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/censatCentromeres.html
@@ -1,63 +1,63 @@
 <h2>Description</h2>
 <p>
 This track shows the active centromere region of each chromosome in this Human
 Pangenome Reference Consortium (HPRC) Release 2 assembly. The centromere is the
 constricted part of a chromosome where the two copies are held together and where
 the spindle attaches to pull them apart during cell division. Within the large
 satellite arrays of each chromosome, one region carries the specialized chromatin
 that actually recruits this machinery; that region is the "active" centromere
 shown here. This is a summarized companion to the more detailed centromere
 satellite (cenSat) track.
 </p>
 
 <h2>Display Conventions</h2>
 <p>
 Each item is the active centromere interval on one sequence, drawn as a simple
 block. There are no sub-features.
 </p>
 
 <h2>Methods</h2>
 <p>
 Active centromere regions were derived from the cenSat annotation of each
 complete assembly, 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 BED file was converted to a UCSC bigBed file. 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>censatCentromeres.bb</tt>) that can be read with the UCSC tool
 <tt>bigBedToBed</tt>. The original files are available from the HPRC S3 bucket
 linked above.
 </p>
 
 <h2>Credits</h2>
 <p>
 Annotations were generated by the Human Pangenome Reference Consortium. Thanks to
 the HPRC production team for making these data available.
 </p>
 
 <h2>References</h2>
 
 
 <p>
 Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov
 FD, Shew CJ <em>et al</em>.
 <a href="https://www.science.org/doi/10.1126/science.abl4178" target="_blank">
 Complete genomic and epigenetic maps of human centromeres</a>.
 <em>Science</em>. 2022 Apr;376(6588):eabl4178.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35357911" target="_blank">35357911</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233505/" target="_blank">PMC9233505</a>
 </p>