ae2a62a18bf9750819f17f8f2237b1f7b1b9911f
lrnassar
  Sat Jun 13 10:48:41 2026 -0700
lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258

Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off
dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept),
and remove the searchIndex name settings that were added by mistake. searchIndex
removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the
lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll
rebuild will drop KimPD from databases.tsv / the merged track.

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 6d1d9eff546..60da0554002 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -23,31 +23,30 @@
 filterLabel.AC Allele Count
 noScoreFilter on
 
     include lrSvAll.ra
 
     track colorsDbSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
     shortLabel CoLoRSdb 1427 SVs
     longLabel Structural Variants from CoLoRSdb (Consortium of Long-Read Sequencing, 1,427 Samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     dataVersion v1.2.0
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$AF AC=$AC/$AN (Hom:$acHom Het:$acHet Hemi:$acHemi) samples=$NS
-    searchIndex name
     filterValues.svType DEL,INS,INV,DUP
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:101381
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:18724
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.AC 0:2854
     filterByRange.AC on
     filterLabel.AC Alt Allele Count (AC)
     filter.AF 0:1
     filterByRange.AF on
     filterLimits.AF 0:1
@@ -381,71 +380,77 @@
     filter.AC 1:136
     filterByRange.AC on
     filterLabel.AC Allele Count (carrier haplotypes)
     filter.sampleCount 1:65
     filterByRange.sampleCount on
     filterLabel.sampleCount Sample Count
     filterValues.refTrf True,False
     filterType.refTrf multipleListOr
     filterLabel.refTrf In Tandem Repeat
     filter.refSd 0:1
     filterByRange.refSd on
     filterLimits.refSd 0:1
     filterLabel.refSd Segmental Duplication Overlap
     skipEmptyFields on
 
-    track kwanhoSv
-    parent lrSv
-    bigDataUrl /gbdb/$D/lrSv/kwanho.bb
-    shortLabel Kim PD 100 prelim
-    longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using
-    type bigBed 9 +
-    itemRgb on
-    visibility dense
-    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC AF_PD=$afPd AF_HC=$afHc diff=$differentialRate
-    filterValues.svType DEL,INS,DUP,INV
-    filterType.svType multipleListOr
-    filterLabel.svType SV Type
-    filter.svLen 0:200000000
-    filterByRange.svLen on
-    filterLabel.svLen SV Length
-    filter.insLen 0:20145
-    filterByRange.insLen on
-    filterLabel.insLen Insertion Length
-    filter.AC 0:200
-    filterByRange.AC on
-    filterLabel.AC Allele Count (PD+HC+ILBD)
-    filter.qual 0:100
-    filterByRange.qual on
-    filterLabel.qual Quality
-    filter.afPd 0:1
-    filterByRange.afPd on
-    filterLimits.afPd 0:1
-    filterLabel.afPd Allele Frequency (PD)
-    filter.afHc 0:1
-    filterByRange.afHc on
-    filterLimits.afHc 0:1
-    filterLabel.afHc Allele Frequency (HC)
-    filter.afIlbd 0:1
-    filterByRange.afIlbd on
-    filterLimits.afIlbd 0:1
-    filterLabel.afIlbd Allele Frequency (ILBD)
-    filter.differentialRate -1:1
-    filterByRange.differentialRate on
-    filterLimits.differentialRate -1:1
-    filterLabel.differentialRate Case-Control Differential (case - control)
-    skipEmptyFields on
+    # kwanhoSv commented out: the Kim PD brain callset is preliminary and
+    # unpublished (the description page says do not release until publication),
+    # and carries breakend artifacts up to ~190 Mb. Held off dev/alpha until a
+    # paper is out. bigBed, .as, converter and makeDoc are retained. The
+    # pending lrSvAll rebuild will also drop KimPD from databases.tsv so it
+    # leaves the merged track. refs #36258
+    #track kwanhoSv
+    #parent lrSv
+    #bigDataUrl /gbdb/$D/lrSv/kwanho.bb
+    #shortLabel Kim PD 100 prelim
+    #longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using
+    #type bigBed 9 +
+    #itemRgb on
+    #visibility dense
+    #mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC AF_PD=$afPd AF_HC=$afHc diff=$differentialRate
+    #filterValues.svType DEL,INS,DUP,INV
+    #filterType.svType multipleListOr
+    #filterLabel.svType SV Type
+    #filter.svLen 0:200000000
+    #filterByRange.svLen on
+    #filterLabel.svLen SV Length
+    #filter.insLen 0:20145
+    #filterByRange.insLen on
+    #filterLabel.insLen Insertion Length
+    #filter.AC 0:200
+    #filterByRange.AC on
+    #filterLabel.AC Allele Count (PD+HC+ILBD)
+    #filter.qual 0:100
+    #filterByRange.qual on
+    #filterLabel.qual Quality
+    #filter.afPd 0:1
+    #filterByRange.afPd on
+    #filterLimits.afPd 0:1
+    #filterLabel.afPd Allele Frequency (PD)
+    #filter.afHc 0:1
+    #filterByRange.afHc on
+    #filterLimits.afHc 0:1
+    #filterLabel.afHc Allele Frequency (HC)
+    #filter.afIlbd 0:1
+    #filterByRange.afIlbd on
+    #filterLimits.afIlbd 0:1
+    #filterLabel.afIlbd Allele Frequency (ILBD)
+    #filter.differentialRate -1:1
+    #filterByRange.differentialRate on
+    #filterLimits.differentialRate -1:1
+    #filterLabel.differentialRate Case-Control Differential (case - control)
+    #skipEmptyFields on
 
     track aprSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/apr.bb
     shortLabel Arab APR 53 SVs
     longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99885
     filterByRange.svLen on
@@ -509,31 +514,30 @@
     filterByRange.geneCount on
     filterLabel.geneCount Gene Count
     skipEmptyFields on
 
     # NOT FOR RELEASE: data received from Eichler lab via email, not yet published.
     # Do not add to lrSvAll merged track until a preprint or paper is available.
     track lrSv1kLin
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/lin1218.bb
     shortLabel 1KG Linear 1218 SVs
     longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear Long-read)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$AN AF=$AF AF_AFR=$afAfr AF_EUR=$afEur samples=$NS
-    searchIndex name
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99565
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:99968
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.AC 0:2436
     filterByRange.AC on
     filterLabel.AC Allele Count
     filter.AF 0:1
     filterByRange.AF on
     filterLimits.AF 0:1