# trackDb stanzas for the hprc2annot GenArk contributed track collection.
# HPRC Release 2 annotations on the ~462 HPRC assembly hubs, refs #35415.
#
# hprc2annotMakeTrackDb.py reads this file, keeps only the stanzas whose
# bigDataUrl file is present in a given assembly's hub directory, and writes
# the per-assembly trackDb.txt. Stanzas are separated by blank lines; comment
# lines are ignored. Paths here are relative to the assembly's hub directory;
# genark addContrib rewrites them to contrib/hprc2annot/... when it wires the
# collection into each assembly's hub.txt.
#
# dataVersion values come from the HPRC index CSV file names (see the makeDoc,
# src/hg/makeDb/doc/contrib/hprc2annot/hprc2annot.txt); update them when HPRC reissues a
# track.

track hprcCatGenes
shortLabel CAT Genes
longLabel CAT (Comparative Annotation Toolkit) gene annotations
type bigGenePred
bigDataUrl catGenes.bb
group genes
priority 10
visibility pack
labelFields name,name2
defaultLabelFields name2
searchIndex name,name2
baseColorDefault genomicCodons
dataVersion HPRC Release 2, CAT genes v1.3
html ../docs/catGenes

track hprcLiftoffGenes
shortLabel Liftoff Genes
longLabel Liftoff RefSeq gene annotations
type bigGenePred
bigDataUrl liftoffGenes.bb
group genes
priority 11
visibility dense
labelFields name,name2
defaultLabelFields name2
searchIndex name,name2
baseColorDefault genomicCodons
dataVersion HPRC Release 2, Liftoff genes v1.0
html ../docs/liftoffGenes

track hprcCensat
shortLabel cenSat
longLabel Centromere satellite annotation (cenSat)
type bigBed 9 +
bigDataUrl censat.bb
group varRep
priority 20
visibility pack
itemRgb on
searchIndex name
dataVersion HPRC Release 2, cenSat v1.0
html ../docs/censat

track hprcActiveCentromeres
shortLabel Active Centromere
longLabel Active centromere regions
type bigBed 3
bigDataUrl censatCentromeres.bb
group map
priority 21
visibility dense
color 220,20,60
dataVersion HPRC Release 2, cenSat centromeres v1.0
html ../docs/censatCentromeres

track hprcSegdups
shortLabel Seg Dups
longLabel Segmental duplications (SEDEF)
type bigBed 9 +
bigDataUrl segdups.bb
group varRep
priority 22
visibility dense
itemRgb on
filterValues.original True,False
filterType.original multipleListOr
filterLabel.original SEDEF original call
mouseOver Duplicate of ${partner}<br>Identity: ${pctMatch}%<br>Aligned length: ${alnLen} bp<br>Satellite bases: ${satBases}
dataVersion HPRC Release 2, SEDEF segdups v1.1
html ../docs/segdups

track hprcPclai
shortLabel PCLAI Ancestry
longLabel Point cloud local ancestry inference (PCLAI)
type bigBed 9 +
bigDataUrl pclai.bb
group compGeno
priority 30
visibility dense
onlyVisibility dense
denseClick on
itemRgb on
mouseOver Window ${window}<br>Window PC1,PC2: ${pca}<br>Ancestry centroid: ${centroid}<br>Confidence: ${score}
dataVersion HPRC Release 2, PCLAI v1.1
detailsScript.scatterPlot.pca {"dataUrl":"../pclaiRefPanel.json","exportFields":["pca","centroid"],"title":"Position in ancestry space","xLabel":"PC1","yLabel":"PC2"}
html ../docs/pclai

track hprcMethylation
shortLabel Methylation
longLabel ONT 5mC CpG methylation
type bigWig 0 100
bigDataUrl methylation.bw
group regulation
priority 40
visibility full
autoScale off
viewLimits 0:100
maxHeightPixels 100:40:8
color 0,0,200
dataVersion HPRC Release 2, ONT methylation v1.0
html ../docs/methylation
