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/methylation.html src/hg/makeDb/trackDb/contrib/hprc2annot/methylation.html
index c4b35761608..911149be5ff 100644
--- src/hg/makeDb/trackDb/contrib/hprc2annot/methylation.html
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/methylation.html
@@ -21,31 +21,31 @@
 <h2>Methods</h2>
 <p>
 Oxford Nanopore reads (R9.4.1 chemistry) were aligned to the assembly with
 minimap2, per-read 5-methylcytosine calls were summarized to a per-CpG
 methylation frequency, and the frequencies were stored as a bigWig signal track.
 See Credits for the HPRC methylation pipeline.
 </p>
 <p>
 The methylation 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/methylation" target="_blank">the hprc_intermediate_assembly data tables</a>.
 The per-assembly bigWig files are already in bigWig format and are served
 unchanged, with no conversion step. The sequence names in them follow the HPRC
 PanSN convention and are resolved to the assembly through the GenArk chromAlias.
 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>
 The methylation signal is stored as a bigWig file (<tt>methylation.bw</tt>) that
 can be read with the UCSC tools <tt>bigWigInfo</tt> and
 <tt>bigWigToBedGraph</tt>, or queried by region with <tt>bigWigSummary</tt>.
 The original files are available from the HPRC S3 bucket linked above.
 </p>
 
 <h2>Credits</h2>