bf62c01cee8dc176445aa131e2fd6ea847a4eb68
lrnassar
  Thu May 28 11:32:52 2026 -0700
Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648

Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a
bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity
classification. Filters: pathogenicity, variantClassification, variantType,
tumor frequency. Search by HGVS cDNA name and canonical protein change via
extraIndex + trix. Linkouts to COSMIC and dbSNP.

Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips
actually change. Cron-silent on no-op so unchanged weeks don't email.

Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema),
src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza),
src/hg/makeDb/trackDb/human/umdTp53.html (description page),
src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition).

Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated).
Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict
trackDb checker resolves the parent in the same include chain as the
existing mucins children. Drops the redundant locusSpec stanza from
human/mucins.ra now that it lives in its own file.

diff --git src/hg/makeDb/trackDb/human/mucins.ra src/hg/makeDb/trackDb/human/mucins.ra
index 1cc748bd2ad..512ec03d42b 100644
--- src/hg/makeDb/trackDb/human/mucins.ra
+++ src/hg/makeDb/trackDb/human/mucins.ra
@@ -1,22 +1,15 @@
-track locusSpec
-superTrack on
-shortLabel Locus-specific
-longLabel Locus-specific annotations
-group genes
-visibility hide
-
     track mucinsNonVntr
     parent locusSpec
     shortLabel Mucin non-VNTR exons
     longLabel Mucin gene non-VNTR exons (Plender et al. 2024 supplementary data)
     type bigGenePred
     bigDataUrl /gbdb/$D/locusSpec/mucins/mucinsNonVntr.bb
     itemRgb on
     visibility pack
     searchIndex name,name2,geneName
     labelFields name,name2,geneName,geneName2
     defaultLabelFields name
     mouseOver <b>$name2 $name</b><br>transcript: $geneName<br>type: $type<br>length: ${chromEnd}-${chromStart}
     priority 2
 
     track mucinsVntr