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/segdups.html src/hg/makeDb/trackDb/contrib/hprc2annot/segdups.html
index ebc9b3a9c72..3f0400852ce 100644
--- src/hg/makeDb/trackDb/contrib/hprc2annot/segdups.html
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/segdups.html
@@ -45,31 +45,31 @@
 <p>
 Segmental duplications were detected with SEDEF, which finds pairs of homologous
 genomic segments by seeding on shared <i>k</i>-mers and extending and refining
 the alignments, then reports each duplicated segment pair with a set of
 alignment statistics (see reference below). The calls were produced by the
 Eichler laboratory as part of the HPRC assembly annotation.
 </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/segdups" target="_blank">the hprc_intermediate_assembly data tables</a>.
 The per-assembly SEDEF output was converted to a UCSC bigBed file, keeping the
 region coordinates, the paralog partner, and the main alignment statistics. The
 sequence name of the paralogous region is translated from the HPRC PanSN naming
 to the name shown elsewhere in the browser. 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>
 <p>
 Every duplication call in the source files is kept, with one exception. For
 HG00735 haplotype 2 (GCA_018472765.3) the SEDEF calls were computed against an
 earlier version of the assembly's contigs, so about 40,000 contig-level calls
 name sequences that do not exist in the assembly served here and could not be
 placed; the roughly 21,600 chromosome-level calls are unaffected, although about
 half of them name one of the missing contigs as their paralogous region, so on
 that assembly alone the partner is shown in the HPRC naming rather than
 translated. This is a version mismatch in the source data rather than something
 introduced in the conversion. It is the only assembly of the 462 where either