53ab3f1e293a91ddf71ec7568f4a6ff827bcd278
lrnassar
  Fri Oct 2 13:52:36 2026 -0700
Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451

diff --git src/hg/makeDb/trackDb/worm/ce11/trackDb.ra src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
index 7b51742ef14..df5825ab7f9 100644
--- src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
+++ src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
@@ -1,60 +1,62 @@
 # Local declaration so that local gold.html is picked up.
 track gold override
 html gold
 
 # Local declaration so that local gap.html is picked up.
 track gap override
 visibility hide
 html gap
 
 searchTable gold
 shortCircuit 1
 termRegex [ABCFXZ][123456789LOUX][0-9]+(\.[0-9]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
 track rmsk override
 visibility hide
 
 track wormBaseGene
 shortLabel WS245 Genes
 longLabel Genes predictions from WormBase WS245 release
 group genes
 priority 32
 visibility pack
 color 0,0,200
 type genePred
 url http://www.wormbase.org/db/gene/gene?name=$$;class=Gene
 urlLabel WormBase:
 
 searchName wormBaseGene
 searchTable wormBaseGene
 searchType genePred
 searchMethod fuzzy
 # shortCircuit 1
 searchPriority 18
 
 include trackDb.26way.ra
 include trackDb.chainNet.ra
 
 track chainSelf
 shortLabel Self Chain
 longLabel $Organism Chained Self Alignments
 group varRep
 priority 400
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain ce11
 otherDb ce11
 
 # change these two to switch to the new refSeqComposite 2018-02
 #include trackDb.refGene.ra public
 include ../../refSeqComposite.ra
 
 include chainNetNematodes.ra
 include trackDb.135way.ra
 
 # include ce11.GCA_000180635.4.chainNet.ra alpha
 # include ce11.danRer11.chainNet.ra alpha
+
+include gpnStar.ra alpha