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/doc/hs1/lrSv.txt src/hg/makeDb/doc/hs1/lrSv.txt
index d2269d7ebcb..10ea23faa71 100644
--- src/hg/makeDb/doc/hs1/lrSv.txt
+++ src/hg/makeDb/doc/hs1/lrSv.txt
@@ -79,15 +79,22 @@
 bedSort hprc2v21.bed hprc2v21.sorted.bed
 bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2Ro.as \
     -tab hprc2v21.sorted.bed /hive/data/genomes/hs1/chrom.sizes hprc2v21.bb
 
 ##########
 # 2026-06-13 Claude max
 #
 # QA fixes (refs #36258), hs1 side. See doc/hg38/lrSv.txt for the full writeup.
 # The converters now drop byte-identical duplicate rows, so re-running the
 # hs1 builds above gives the new counts:
 #   hprc2v21 hs1  608,435 -> 541,176  (67,259 duplicates dropped)
 # colorsDb hs1 and 1kgOnt hs1 were rebuilt from source for the shared color
 # palette (CPX purple, colorsDb DEL 200,0,0); apr hs1 and cpc1 hs1 only needed
 # the CPX color remapped, so their served bigBeds were recolored in place the
 # same way as the hg38 files (see doc/hg38/lrSv.txt). There is no hs1 lrSvAll.
+
+##########
+# 2026-08/09 - see doc/hg38/lrSv.txt for the dated blocks covering the deletion
+# anchor fix (2026-08, refs #38099), the lrSv1kLin insertion span fix and the
+# filter-cap bumps (2026-09-01, refs #38099). Those rebuilds also replaced the
+# hs1 bigBeds for 1kgOnt, apr, cpc1, colorsDb and lin1218; all of them are
+# built from the hg38 work dirs by the commands in that file.