691aa9e2e4f42cd650b092d338eb7bf67ce97bc4
gperez2
  Sun Oct 27 18:52:19 2024 -0700
Nesting DECIPHER tracks into a single superTrack, refs #34702

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index c7d331d..57f51a8 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -123,67 +123,30 @@
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 color 72,167,38
 searchIndex name,ncbiAcc
 
 track gad
 shortLabel GAD View
 longLabel Genetic Association Studies of Complex Diseases and Disorders
 group phenDis
 visibility hide
 color 200,0,0
 type bed 4
 url http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=
 
-track decipher
-shortLabel DECIPHER CNVs
-longLabel DECIPHER CNVs
-group phenDis
-visibility hide
-type bigBed 9 +
-itemRgb on
-tableBrowser off knownCanonToDecipher knownToDecipher decipherRaw
-bigDataUrl /gbdb/$D/decipher/decipherCnv.bb
-url https://www.deciphergenomics.org/patient/$$
-urlLabel Decipher Patient View:
-filter.size 0
-filterByRange.size on
-filterLimits.size 2:170487333
-filterValues.variant_class Amplification,Copy-Number Gain,Deletion,Duplication,Duplication/Trip
-filterValues.pathogenicity Benign,Likely Benign,Likely Pathogenic,Pathogenic,Uncertain,Unknown
-mergeSpannedItems on
-searchIndex name
-mouseOverField _mouseOver
-
-searchTable decipher
-searchMethod exact
-searchType bigBed
-release alpha,beta
-
-track decipherSnvs
-shortLabel DECIPHER SNVs
-longLabel DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs)
-group phenDis
-visibility hide
-color 0,0,0
-type bed 4
-tableBrowser off decipherSnvsRaw
-prevExonText Left edge
-nextExonText Right edge
-html decipher
-
 track phegeni
 shortLabel PheGenI SNPs
 longLabel NCBI Phenotype-Genotype Integrator SNPs
 group phenDis
 visibility hide
 color 0,100,0
 type bigBed 9 +
 release alpha
 mouseOverField trait
 bigDataUrl /gbdb/$D/bbi/phegeni.bb
 urls studyId=https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$$ geneId1=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D geneId2=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D analysisId=https://www.ncbi.nlm.nih.gov/projects/SNP/gViewer/gView.cgi?aid=$$ catalogId=https://www.ebi.ac.uk/gwas/search?query=$$
 
 track varsInPubs
 shortLabel Variants in Papers
 longLabel Genetic Variants mentioned in scientific publications
@@ -4861,44 +4824,34 @@
         track clinGenTriploSensitivity
         parent doseSensitivity
         shortLabel Triplo Sensitivity
         longLabel ClinGen Triplo Sensitivity
         visibility dense
         priority 2
         type bigBed 9 +
         bigDataUrl /gbdb/$D/doseSensitivity/clinGenTriploSensitivity.bb
         mouseOverField mouseOver
         subGroups view=dose class=path level=cur
 
 include phastBias.ra
 
 include omim.ra
 
-include ../refSeqComposite.ra
+include decipher.alpha.ra alpha
+include decipher.ra beta,public
 
-searchName decipherId
-searchTable decipher
-termRegex [0-9]+
-searchType bed
-searchPriority 50
-release public
-
-searchName decipherSnvsId
-searchTable decipherSnvs
-termRegex [0-9]+
-searchType bed
-searchPriority 50
+include ../refSeqComposite.ra
 
 searchTable ensGene
 searchType genePred
 termRegex ENS([A-Z]{3})?T[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchName ensDotPrefix
 searchTable ensGene
 query select chrom,txStart,txEnd,name from %s where name like '%s.%%'
 termRegex ENS([A-Z]{3})?T[0-9]+
 dontCheck ENS([A-Z]{3})?T[0-9]+\.[0-9]+
 searchPriority 50
 
 searchName ensGeneGtpGene
 searchTable ensGene