b687dd9018670941ce30f8a4582d6597c5a974d8
lrnassar
  Tue Sep 1 14:57:43 2026 -0700
lrSv1kLin: fix 2bp insertion span, drop dead numConsolidated field, refresh lrSvAll merge. refs #38099

The Lin 1218 VCFs set INFO/END = POS+1 on insertions, and the converter took
chromEnd from END, so every insertion was drawn 2bp wide with svLen 2 instead
of the 1bp anchor base. That contradicted the track's own description page and
the coordinate convention in the makeDoc, and it kept 107,980 Lin insertions
from merging in lrSvAll. Insertions now clamp chromEnd to the anchor; deletions
are unchanged and still verify span == |SVLEN| against the source VCFs.

Dropped numConsolidated from the converter and the .as: the NumConsolidated
INFO key is declared in the VCF header but never appears on a data line, so the
column was 0 on all 1.2M rows and added a meaningless line to every detail page.

Rebuilt lin1218 on hg38 and hs1 (item counts and variant names unchanged) and
re-ran the merge: lrSvAll 2,963,093 -> 2,855,267 rows as the duplicate insertion
rows collapse.

Bumped seven filter.svLen/insLen maxima in lrSv.ra that were short of the data
after the August deletion narrowing, three of them only visible on hs1.

lrSvAll.html said the 1000 Genomes linear set was not in the merge, which is no
longer true, and gave no warning that sourceCount double-counts because Lin1218
already absorbs HPRC, HGSVC3 and both 1KG ONT callsets. Corrected the merge key
description and refreshed ten stale cells in the lrSv.html summary table.

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 11a432fa725..c8265b73f02 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -29,31 +29,31 @@
 
     track colorsDbSv
     parent longReadVariants
     priority 1
     bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
     shortLabel CoLoRSdb 1427 SVs
     longLabel Structural Variants from 1,427 CoLoRSdb samples (Consortium of Long-Read Sequencing, PacBio HiFi)
     type bigBed 9 +
     itemRgb on
     visibility hide
     dataVersion v1.2.0
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AF</b>: $AF<br><b>AC</b>: $AC/$AN (Hom $acHom, Het $acHet, Hemi $acHemi)<br><b>Samples</b>: $NS
     filterValues.svType DEL,INS,INV,DUP
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:101381
+    filter.svLen 0:111110
     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
     filterLabel.AF Allele Frequency (AF)
     skipEmptyFields on
 
     track lrSv1kgOnt
@@ -91,31 +91,31 @@
     dataVersion 1.1
 
     track gustafsonSv
     parent longReadVariants
     priority 5
     bigDataUrl /gbdb/$D/lrSv/gustafson.bb
     shortLabel 1KG UW ONT SVs
     longLabel Structural Variants from 100 1000 Genomes samples (University of Washington ONT; Gustafson et al. 2024)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC<br><b>Samples</b>: $sampleCount
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:98289
+    filter.svLen 0:98290
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:25094
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:200
     filterByRange.AC on
     filterLabel.AC Allele Count (placeholder)
     filter.sampleCount 1:100
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Carrier Samples
     skipEmptyFields on
 
     track noyvertSv
     parent longReadVariants
@@ -177,31 +177,31 @@
     skipEmptyFields on
 
     track lrSv1kLin
     parent longReadVariants
     priority 3
     bigDataUrl /gbdb/$D/lrSv/lin1218.bb
     shortLabel 1KG Lin 1218 SVs
     longLabel Structural Variants from 1,218 1000 Genomes samples (long-read merge; Lin et al.)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$AN<br><b>AF</b>: $AF<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur<br><b>Samples</b>: $NS
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:99565
+    filter.svLen 0:99691
     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
     filterLabel.AF Allele Frequency
     filter.afAfr 0:1
     filterByRange.afAfr on
     filterLimits.afAfr 0:1
@@ -261,31 +261,31 @@
     skipEmptyFields on
 
     track han945Sv
     parent longReadVariants
     priority 12
     bigDataUrl /gbdb/$D/lrSv/han945.bb
     shortLabel Han 945 SVs
     longLabel Structural Variants from 945 Han Chinese samples (long-read)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AF</b>: $alleleFreq<br><b>AC</b>: $AC<br><b>Samples</b>: $sampleCount
     filterValues.svType DEL,INS,DUP,INV,TRA
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:99743
+    filter.svLen 0:99744
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:27242
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:1890
     filterByRange.AC on
     filterLabel.AC Allele Count (approx 2*SUPP)
     filter.sampleCount 1:945
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Supporting Samples
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
@@ -320,31 +320,31 @@
     filterLabel.AC Allele Count
 
     track ga4kSv
     parent longReadVariants
     priority 16
     bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb
     shortLabel GA4K 502 SVs
     longLabel Structural Variants from 502 GA4K samples (Children's Mercy, pediatric rare disease; PacBio HiFi)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC (approx)</b>: $AC<br><b>AF</b>: $alleleFreq<br><b>Carriers</b>: $carrierCount/$sampleTotal
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:809711
+    filter.svLen 0:809712
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:14923
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:996
     filterByRange.AC on
     filterLabel.AC Allele Count (approx)
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.carrierCount 1:498
     filterByRange.carrierCount on
     filterLabel.carrierCount Number of Carrier Samples
@@ -557,61 +557,61 @@
     skipEmptyFields on
 
     track aprSv
     parent longReadVariants
     priority 15
     bigDataUrl /gbdb/$D/lrSv/apr.bb
     shortLabel Arab APR 53 SVs
     longLabel Structural Variants from 53 Arab Pangenome Reference samples (UAE-resident; HiFi + ONT)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:99885
+    filter.svLen 0:99892
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:584016
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:107
     filterByRange.AC on
     filterLabel.AC Allele Count
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
 
     track cpc1Sv
     parent longReadVariants
     priority 13
     bigDataUrl /gbdb/$D/lrSv/cpc1.bb
     shortLabel CPC 58 SVs
     longLabel Structural Variants from 58 Chinese Pangenome Consortium samples (CPC-only; HiFi)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:8998096
     filterByRange.svLen on
     filterLabel.svLen SV Length
-    filter.insLen 0:376583
+    filter.insLen 0:414249
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:116
     filterByRange.AC on
     filterLabel.AC Allele Count
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
 
     track chirmade101Sv
     parent longReadVariants
     priority 17
     bigDataUrl /gbdb/$D/lrSv/chirmade101.bb
     shortLabel SVatalog 101 SVs