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/scripts/hprc2annot/pclai.as src/hg/makeDb/scripts/hprc2annot/pclai.as
new file mode 100644
index 00000000000..1488c5472cc
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2annot/pclai.as
@@ -0,0 +1,16 @@
+table pclai
+"HPRC point-cloud local ancestry inference (pcLAI), assembly coordinates"
+    (
+    string chrom;      "Reference sequence chromosome or scaffold"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "Unused (values are shown on mouseover)"
+    uint   score;      "Confidence score (0-1000)"
+    char[1] strand;    "+ or -"
+    uint   thickStart; "Start of thick drawing"
+    uint   thickEnd;   "End of thick drawing"
+    uint   reserved;   "Item color (R,G,B)"
+    string window;     "Local ancestry window id"
+    string pca;        "Window PCA|PCA-space coordinates (PC1,PC2) of this window"
+    string pcaSegment; "Segment PCA|PCA-space coordinates (PC1,PC2) of the containing ancestry segment"
+    )