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/scripts/lrSv/lrSv1kLin1218.as src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as
index 6249d903e31..f181f90dd72 100644
--- src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as
+++ src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as
@@ -10,17 +10,16 @@
     uint thickStart;           "Thick start (same as chromStart)"
     uint thickEnd;             "Thick end (same as chromEnd)"
     uint reserved;             "Item color"
     string svType;             "SV Type|DEL or INS"
     int svLen;                 "SV Length|Length of the variant on the reference in base pairs"
     int insLen;                "Insertion Length|Length of inserted sequence, 0 for DEL"
     int AC;                    "Allele Count|Number of alternate alleles observed"
     int AN;                    "Allele Number|Total number of alleles in called genotypes"
     float AF;                  "Allele Frequency|Overall allele frequency across all samples"
     float afAfr;               "AF African|Allele frequency in African samples"
     float afAmr;               "AF Admixed American|Allele frequency in Admixed American samples"
     float afEas;               "AF East Asian|Allele frequency in East Asian samples"
     float afEur;               "AF European|Allele frequency in European samples"
     float afSas;               "AF South Asian|Allele frequency in South Asian samples"
     int NS;                    "Sample Count|Number of samples with genotype data"
-    int numConsolidated;       "Consolidated Samples|Number of samples consolidated into this call by Truvari"
     )