50466766840ded6cb8bd5cb868bdf2ff3f613bc0
lrnassar
  Tue Apr 21 11:17:15 2026 -0700
QA fixes for PrimateAI-3D track.

Config (primateAi.ra):
- Fix broken Ensembl transcript linkout: urls $S expanded to chromosome
name; switch to the Ensembl transcript page with $$
- Add numeric filters on percentile and raw score (label notes the
paper's 0.821 clinical threshold)
- Add maxWindowToDraw 2000000

Data (primateAiToBigBed.py):
- Change hardcoded strand '+' to '.': the source file has no strand
column
- Accept input/output paths as CLI args (previously hardcoded the hg38
input path)
- Handle variable field count: ~2.4M rows in the hg19 source are
missing the refseq column

Description (primateAi.html):
- Fix two broken hgTrackUi&... internal links to the Zoonomia 447-way
track
- Regenerate the first reference via getTrackReferences (wrong article
number and wrong PMC ID in the previous text)
- Fix the GitHub URL for the conversion script in Methods
- Move the Zoonomia 447-way mention out of Description; rephrase the
license note to describe precisely what is disabled

relatedTracks.ra:
- Add reciprocal cross-links for primateAi <-> alphaMissense (hg38),
primateAi <-> revel (hg38 + hg19), and primateAi <-> promoterAi
(hg38). Also includes promoterAi <-> alphaMissense cross-links.

refs #37274 #37279

diff --git src/hg/makeDb/trackDb/human/primateAi.ra src/hg/makeDb/trackDb/human/primateAi.ra
index 1aebe8e581a..0c5a835abd4 100644
--- src/hg/makeDb/trackDb/human/primateAi.ra
+++ src/hg/makeDb/trackDb/human/primateAi.ra
@@ -1,15 +1,24 @@
 track primateAi
 shortLabel PrimateAI-3D
 longLabel PrimateAI-3D Pathogenicity Predictions for Missense Variants
 type bigBed 9 +
 parent predictionScoresSuper
 bigDataUrl /gbdb/$D/primateAi/primateAi.bb
 itemRgb on
 visibility dense
 tableBrowser off
 scoreFilter 0
 scoreFilterLimits 0:1000
 mouseOverField _mouseOver
 filterValues.prediction benign|Benign,pathogenic|Pathogenic
 filterLabel.prediction Prediction
-urls gene="hgTrackUi?g=knownGene&hgt_tSearch=$S" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$"
+filter.percentile 0
+filterLimits.percentile 0:1
+filterByRange.percentile on
+filterLabel.percentile Percentile score
+filter.scorePAI3D 0
+filterLimits.scorePAI3D 0:1
+filterByRange.scorePAI3D on
+filterLabel.scorePAI3D PrimateAI-3D raw score (clinical threshold 0.821)
+maxWindowToDraw 2000000
+urls gene="https://www.ensembl.org/Homo_sapiens/Transcript/Summary?t=$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$"