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/catGenes.html src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html
index 1845dea164b..9d634359a66 100644
--- src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html
@@ -28,31 +28,31 @@
 The Comparative Annotation Toolkit projects an existing high-quality reference
 annotation onto a target genome through a whole-genome (Cactus/progressiveCactus)
 alignment, reconciles the projected transcripts with <i>ab initio</i> and
 transcript-based evidence, and produces a filtered consensus gene set with
 stable cross-assembly identifiers. See the reference below for the full
 algorithm. For the HPRC pangenome, CAT was run against the CHM13/GRCh38-based
 reference annotation to annotate each assembly.
 </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/cat" target="_blank">the hprc_intermediate_assembly data tables</a>.
 Each per-assembly GFF3 was converted to a UCSC bigGenePred file with
 <tt>gff3ToGenePred</tt> and <tt>genePredToBigGenePred</tt>; gene symbols and gene
 and transcript biotypes from the GFF3 were carried into the display fields. 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>catGenes.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. It can
 also extract features for a region, for example:
 <tt>bigBedToBed catGenes.bb -chrom=CM085953.1 -start=0 -end=100000 stdout</tt>.
 The original annotation files are available from the HPRC S3 bucket linked above.
 </p>