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.html src/hg/makeDb/trackDb/human/lrSv.html
index 513038ec8bf..813450a9316 100644
--- src/hg/makeDb/trackDb/human/lrSv.html
+++ src/hg/makeDb/trackDb/human/lrSv.html
@@ -39,31 +39,31 @@
   <th>N samples</th>
   <th>Cohort / disease</th>
   <th>Disease cases</th>
   <th>Coverage</th>
   <th>SV count</th>
   <th>Min</th>
   <th>Median</th>
   <th>Max</th>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=lrSvAll"><b>All merged</b></a></td>
   <td>&mdash;</td>
   <td>All long-read SV datasets merged on identical position+type+length, with per-database AC</td>
   <td>mixed</td>
   <td>mixed (HiFi, ONT)</td>
-  <td>3,111,026</td>
+  <td>2,855,267</td>
   <td>1</td>
   <td>1</td>
   <td>57,207,413</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb</a></td>
   <td>1,427</td>
   <td>Consortium of Long-Read Sequencing, joint callset</td>
   <td>No</td>
   <td>mixed (HiFi)</td>
   <td>426,239</td>
   <td>20</td>
   <td>33</td>
   <td>101,381</td>
 </tr>
@@ -83,44 +83,44 @@
   <td>1,218</td>
   <td>1000 Genomes long-read merge (HiFi assemblies + ONT), Lin et al.</td>
   <td>No</td>
   <td>mixed (HiFi assembly, ONT R9/R10)</td>
   <td>587,779</td>
   <td>50</td>
   <td>171</td>
   <td>99,968</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=lrSv1kgOnt">1KG Vienna ONT</a></td>
   <td>1,019</td>
   <td>1000 Genomes, diverse</td>
   <td>No</td>
   <td>~17x ONT</td>
-  <td>148,375</td>
+  <td>148,421</td>
   <td>2</td>
-  <td>157</td>
-  <td>49,171</td>
+  <td>156</td>
+  <td>49,170</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=gustafsonSv">1KG UW ONT</a></td>
   <td>100</td>
   <td>1000 Genomes, 5 superpopulations / 19 subpopulations (University of Washington ONT effort)</td>
   <td>No</td>
   <td>~37x ONT (R9.4.1)</td>
   <td>113,159</td>
   <td>1</td>
-  <td>167</td>
+  <td>166</td>
   <td>98,290</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=noyvertSv">1KG Boehringer ONT 888</a></td>
   <td>888</td>
   <td>1000 Genomes, 5 superpopulations; used to impute SVs into ~500,000 UK Biobank participants</td>
   <td>No</td>
   <td>~15x ONT (R9.4.1)</td>
   <td>107,445</td>
   <td>1</td>
   <td>1</td>
   <td>28,634,664</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1</a></td>
@@ -162,73 +162,73 @@
   <td>No</td>
   <td>~40x ONT (R9.4.1 / R10.4.1)</td>
   <td>228,855</td>
   <td>1</td>
   <td>1</td>
   <td>30,282,742</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=decodeSv">deCODE 3,622</a></td>
   <td>3,622</td>
   <td>Icelandic general population, no allele counts</td>
   <td>No</td>
   <td>~17x ONT</td>
   <td>119,453</td>
   <td>1</td>
-  <td>154</td>
-  <td>861,081</td>
+  <td>152</td>
+  <td>861,080</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=han945Sv">Han 945</a></td>
   <td>945</td>
   <td>Han Chinese, general population</td>
   <td>No</td>
   <td>~17x ONT</td>
   <td>111,288</td>
   <td>1</td>
   <td>254</td>
   <td>99,744</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=cpc1Sv">CPC</a></td>
   <td>58</td>
   <td>Chinese Pangenome Consortium, 36 minority ethnic groups (HPRC-specific SVs removed)</td>
   <td>No</td>
   <td>~30x HiFi (pangenome graph)</td>
-  <td>36,030</td>
+  <td>36,045</td>
   <td>50</td>
-  <td>134</td>
+  <td>130</td>
   <td>8,998,096</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=tommoJpSv">ToMMo Japanese</a></td>
   <td>333 (111 trios)</td>
   <td>Japanese, general population</td>
   <td>No</td>
   <td>~22x ONT</td>
   <td>74,201</td>
   <td>51</td>
   <td>158</td>
   <td>99,985</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=aprSv">Arab APR</a></td>
   <td>53</td>
   <td>UAE-resident Arabs from 8 countries (Arab Pangenome Reference)</td>
   <td>No</td>
   <td>~35x HiFi + ~54x ONT (+ Hi-C, pangenome graph)</td>
-  <td>72,656</td>
+  <td>72,662</td>
   <td>1</td>
   <td>121</td>
   <td>584,016</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=ga4kSv">GA4K</a></td>
   <td>502</td>
   <td>Children's Mercy, pediatric rare disease probands + families</td>
   <td>Yes (probands)</td>
   <td>~27x HiFi</td>
   <td>115,554</td>
   <td>50</td>
   <td>186</td>
   <td>809,712</td>
 </tr>