fcb3dd044df301a3c0ea4588e1debf7068b00333
lrnassar
  Mon Jun 29 15:43:06 2026 -0700
lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258

Audit fixes:
- lrSv.html summary table: recompute the per-dataset min/median/max SV-length
columns from current data (length = max(svLen,insLen)); the old values came
from the .ra filter bounds and were off by one in several rows. Fixes the
stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was
dropped from the merge) and the APR row's length convention.
- decodeSv.html: align the opening Description to the displayed (deduped) counts
(119,453 / 41,216 DEL) instead of the upstream release counts, noting the
dedup from the 133,886-record release.
- Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack,
from the lrSv supertrack filterValues.svType and from lrSvAll (both the
generated lrSvAll.ra and the lrSvMergeAll.py generator).

Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label
HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each
track's existing fields.

diff --git src/hg/makeDb/trackDb/human/lrSvAll.ra src/hg/makeDb/trackDb/human/lrSvAll.ra
index 220e5911871..bf2c5bd32fa 100644
--- src/hg/makeDb/trackDb/human/lrSvAll.ra
+++ src/hg/makeDb/trackDb/human/lrSvAll.ra
@@ -1,40 +1,40 @@
 # AUTO-GENERATED by ~/kent/src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
 # Do not edit by hand - re-run the merge script and re-commit.
 
     track lrSvAll
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/lrSvAll.bb
     shortLabel All LR SVs merged
     longLabel All long-read SVs merged across subtracks by exact position, with per-database AC
     type bigBed 9 +
     itemRgb on
     visibility pack
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Sources</b>: $sources<br><b>AF range</b>: $minAF-$maxAF<br><b>AC</b>: $AC
     filterValues.sources CoLoRSdb|CoLoRSdb 1427 (PacBio),1000G-ONT-Vienna|1KG ONT Vienna 1019,1000G-ONT|1KG ONT 100 (Gustafson),AoU1K|All of Us 1027 (PacBio),Han945|Han Chinese 945,TommoJapan|ToMMo 333 (Japanese),GA4K|GA4K 502 (rare disease),deCODE|deCODE 3622 (Icelandic),HPRCv2.1|HPRC v2.1 233,HGSVC2|HGSVC2 32,HGSVC3|HGSVC3 65,ArabUAE53|Arab APR 53,China58|CPC 58 (Chinese),Svatalog101|SVatalog 101
     filterType.sources multipleListOr
     filterLabel.sources Source Database
-    filterValues.svType DEL,INS,DUP,INV,CPX,MIXED,INSDEL,CNV,BND,TRA,MEI
+    filterValues.svType DEL,INS,DUP,INV,CPX,MIXED,INSDEL,TRA
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:30000000
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:600000
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.maxAF 0:1
     filterByRange.maxAF on
     filterLimits.maxAF 0:1
     filterLabel.maxAF Max Allele Frequency (across DBs)
     filter.minAF 0:1
     filterByRange.minAF on
     filterLimits.minAF 0:1
     filterLabel.minAF Min Allele Frequency (across DBs)
     filter.AC 0:30000
     filterByRange.AC on
     filterLabel.AC Total AC (across DBs)
     filter.sourceCount 1:14
     filterByRange.sourceCount on
     filterLabel.sourceCount Number of Source Databases
     skipEmptyFields on
     priority 0