e6d1189bea4cc541396f842b65a3392c33c8e734
max
  Wed Sep 2 02:55:03 2026 -0700
hprc2annot: put the collection in git and fix the QA findings

The HPRC Release 2 GenArk contributed track collection (7 tracks x 462
assemblies) had only its one-line betaGenArk.txt enable checked in. Add the
makeDoc, the build scripts, the seven track description pages and the trackDb
stanzas, and fix the problems QA found.

Data fixes, both rebuilt across all 462 assemblies:

- liftoff: gff3ToGenePred was naming each genePred after the gene, so every
transcript of a gene shared one name, the RefSeq accession was lost and the
transcript_biotype lookup never matched (type empty on 99.8% of rows). Pass
-rnaNameAttr=ID. Duplicate (chrom,start,end,name) tuples go from 24,969 to 0
and type is now empty on 2,132 of 82,973,730 rows. The same flag is a no-op
on the CAT GFF3 (byte-identical output), so both gene tracks now share one
code path and CAT needs no rebuild.

- segdups: the build read SEDEF column 6, strand1, which is "+" by construction
on every row, so every inverted duplication rendered forward. Use column 14,
strand2, the orientation of the paralogous copy: 13.8M + and 13.8M - across
the collection. Also translate the paralog partner out of PanSN through the
GenArk chromAlias, since the browser does not translate a plain text field,
and store identity as a percentage so the mouseover can read it.

hprc2annotFixBed.sh is not idempotent for pclai: a second run re-parses an
already-parsed name and blanks the values. It now refuses to touch a converted
file. GCA_041900255.1 was damaged that way and is rebuilt from source.

Provenance, all from the QA report:

- stats.tsv is appended to rather than truncated on every run, and each run
regenerates log/summary.tsv, a per-track roll-up over the collection.
- dataVersion on all seven tracks.
- Rows are now dropped for exactly two reasons and both are counted: past the
end of the sequence, or a sequence name absent from the assembly, which also
warns with example names. Only GCA_018472765.3 trips the second, the known
upstream contig-version mismatch. genePredToBigGenePred failure is checked
and an empty conversion result is a failure, not a valid empty bigBed.

Description pages: fix a raw UTF-8 character, rewrite the segdups and pclai
display conventions which still described the data before the name field was
blanked, add a color legend checked against the data, add the pcLAI preprint
(from the Crossref record, since it has no PMID), and correct the stated reason
liftoff drops transcripts.

Display: title case on the short labels, "Active centromeres" shortened to fit
the 17-character limit, pcLAI to pack since it has no readable dense state,
liftoff and segdups to dense, and a filter on the segdups original flag.

refs #35415

diff --git src/hg/makeDb/trackDb/contrib/hprc2annot/methylation.html src/hg/makeDb/trackDb/contrib/hprc2annot/methylation.html
new file mode 100644
index 00000000000..c4b35761608
--- /dev/null
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/methylation.html
@@ -0,0 +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>,
+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>