af23c5696568feae4289008ed5606a7055def77b
lrnassar
  Sat Jun 13 09:43:01 2026 -0700
lrSv: comment out the hprc2JasmineSv stanza (test callset, not for release). refs #36258

The Jasmine-merged HPRC v2 multi-caller set is a comparison/test callset that
is not slated for release, so its trackDb stanza is commented out rather than
shipped on dev/alpha. The bigBed, autoSql, converter and makeDoc are retained
for reference. The lrSv1kLin stanza is left in place pending confirmation.

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index e66a29dacc5..6d1d9eff546 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -275,65 +275,69 @@
     filter.insLen 0:1064897
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:463
     filterByRange.AC on
     filterLabel.AC Allele Count
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.snarlLevel 0:7
     filterByRange.snarlLevel on
     filterLabel.snarlLevel Snarl Level
     skipEmptyFields on
 
-    track hprc2JasmineSv
-    parent lrSv
-    bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb
-    shortLabel HPRC2 Jasmine 231 SVs
-    longLabel Structural Variants from 231 HPRC v2 Assemblies (Jasmine merge of 14 SV callers)
-    type bigBed 9 +
-    itemRgb on
-    visibility dense
-    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers)
-    filterValues.svType DEL,INS
-    filterType.svType multipleListOr
-    filterLabel.svType SV Type
-    filter.svLen 0:30176500
-    filterByRange.svLen on
-    filterLabel.svLen SV Length
-    filter.insLen 0:30176500
-    filterByRange.insLen on
-    filterLabel.insLen Insertion Length
-    filter.AC 0:231
-    filterByRange.AC on
-    filterLabel.AC Carrier Sample Count
-    filter.alleleFreq 0:1
-    filterByRange.alleleFreq on
-    filterLimits.alleleFreq 0:1
-    filterLabel.alleleFreq Carrier Frequency
-    filter.nCallers 1:14
-    filterByRange.nCallers on
-    filterLabel.nCallers Number of Supporting Callers
-    filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish
-    filterType.callers multipleListAnd
-    filterLabel.callers Supporting Callers
-    filterValues.sources PAV,dipcall,longcallD
-    filterType.sources multipleListAnd
-    filterLabel.sources Source Pipeline
-    skipEmptyFields on
+    # hprc2JasmineSv commented out: the Jasmine-merged HPRC v2 multi-caller
+    # set is a test/comparison callset (the Hall lab is not happy with it) and
+    # is not for release. bigBed, .as, converter and makeDoc are retained.
+    # refs #36258
+    #track hprc2JasmineSv
+    #parent lrSv
+    #bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb
+    #shortLabel HPRC2 Jasmine 231 SVs
+    #longLabel Structural Variants from 231 HPRC v2 Assemblies (Jasmine merge of 14 SV callers)
+    #type bigBed 9 +
+    #itemRgb on
+    #visibility dense
+    #mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers)
+    #filterValues.svType DEL,INS
+    #filterType.svType multipleListOr
+    #filterLabel.svType SV Type
+    #filter.svLen 0:30176500
+    #filterByRange.svLen on
+    #filterLabel.svLen SV Length
+    #filter.insLen 0:30176500
+    #filterByRange.insLen on
+    #filterLabel.insLen Insertion Length
+    #filter.AC 0:231
+    #filterByRange.AC on
+    #filterLabel.AC Carrier Sample Count
+    #filter.alleleFreq 0:1
+    #filterByRange.alleleFreq on
+    #filterLimits.alleleFreq 0:1
+    #filterLabel.alleleFreq Carrier Frequency
+    #filter.nCallers 1:14
+    #filterByRange.nCallers on
+    #filterLabel.nCallers Number of Supporting Callers
+    #filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish
+    #filterType.callers multipleListAnd
+    #filterLabel.callers Supporting Callers
+    #filterValues.sources PAV,dipcall,longcallD
+    #filterType.sources multipleListAnd
+    #filterLabel.sources Source Pipeline
+    #skipEmptyFields on
 
     track hgsvc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb
     shortLabel HGSVC2 32 SVs
     longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 2021)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC AF=$popAllAf
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:57207414
     filterByRange.svLen on