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/umdTp53.ra src/hg/makeDb/trackDb/human/umdTp53.ra
new file mode 100644
index 00000000000..02c9a2f5fdf
--- /dev/null
+++ src/hg/makeDb/trackDb/human/umdTp53.ra
@@ -0,0 +1,28 @@
+    track umdTp53
+    parent locusSpec
+    shortLabel UMD TP53
+    longLabel UMD TP53 Variant Database (p53.fr) - Locus-Specific Variants
+    type bigBed 9 + 43
+    bigDataUrl /gbdb/$D/bbi/umdTp53/umdTp53.bb
+    itemRgb on
+    mouseOverField _mouseOver
+    searchTrix /gbdb/$D/bbi/umdTp53/umdTp53.ix
+    searchIndex name
+    noScoreFilter on
+    visibility pack
+    priority 3
+    html umdTp53
+    urls cosmicId="https://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$"
+    filterValues.pathogenicity Pathogenic,Likely Pathogenic,Possibly pathogenic,VUS,Benign,Unknown
+    filterType.pathogenicity multipleListOr
+    filterLabel.pathogenicity Pathogenicity Classification
+    filterValues.variantClassification Missense,Nonsense,Synonymous,Frameshift_Ins,Frameshift_Del,Frameshift_Indel,In_frame_Ins,In_frame_Del,Complex_Del,Nonstop,Splice,Intronic,UTR,Flank,Gene_Deletion,Other
+    filterType.variantClassification multipleListOr
+    filterLabel.variantClassification Variant Classification
+    filterValues.variantType SNP,DEL,INS,DNP,TNP,ONP
+    filterType.variantType multipleListOr
+    filterLabel.variantType Variant Type
+    filter.tumorFreq 0
+    filterByRange.tumorFreq on
+    filterLimits.tumorFreq 0:10
+    filterLabel.tumorFreq Minimum Tumor Frequency (%)