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
@@ -1,62 +1,62 @@
 <h2>Description</h2>
 <p>
 This track shows DNA methylation across this Human Pangenome Reference Consortium
 (HPRC) Release 2 assembly, measured from Oxford Nanopore (ONT) long-read
 sequencing. Methylation is a chemical mark (a methyl group) added to cytosine
 bases, most often where a C is followed by a G (a "CpG" site). It is a major
 layer of epigenetic regulation: densely methylated promoters tend to be silenced,
 while unmethylated CpG islands are typically active. Nanopore sequencing detects
 these marks directly from the raw signal, so methylation can be read off the same
 reads used to assemble the genome. The track shows, at each CpG, the fraction of
 reads that were methylated.
 </p>
 
 <h2>Display Conventions</h2>
 <p>
 The track is a signal graph. At each position the value is the percentage of
 reads methylated at that CpG, on a 0 to 100 scale. Taller bars mean a higher
 fraction of methylated molecules.
 </p>
 
 <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>
 <p>
 Data were generated by the Human Pangenome Reference Consortium. Thanks to the
 HPRC production team for making these data available.
 </p>
 
 <h2>References</h2>
 <p>
 Method details for the HPRC methylation pipeline are maintained with the
 <a href="https://github.com/human-pangenomics/hprc_intermediate_assembly" target="_blank">HPRC intermediate assembly</a>
 resources. Data were generated by the Human Pangenome Reference Consortium.
 </p>