bac95a147f49cd331052e597006e04b3deee40fc
max
  Wed Apr 22 10:43:20 2026 -0700
lrSv/srSv: human-readable SV type filter labels, script cleanups

Add human-readable labels to the supertrack-level svType filter on
both the lrSv and srSv supertracks using the "CODE|CODE (Long name)"
filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)",
etc. Labels keep the short code up front so users can match what
hgTracks shows next to each feature.

Also sweep in the in-progress converter/as-file cleanups under
scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py
helpers, consistent insLen / svLen / AC column naming, tightened
field-description text) that had been piling up as an unstaged
working tree.

refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSvGustafson.as src/hg/makeDb/scripts/lrSv/lrSvGustafson.as
index 4196e8f9bf9..6284c533e81 100644
--- src/hg/makeDb/scripts/lrSv/lrSvGustafson.as
+++ src/hg/makeDb/scripts/lrSv/lrSvGustafson.as
@@ -1,19 +1,21 @@
 table lrSvGustafson
 "Gustafson 2024 1000 Genomes ONT long-read structural variants (100 samples)"
     (
     string chrom;           "Chromosome"
     uint chromStart;        "Start position"
     uint chromEnd;          "End position"
     string name;            "Variant ID"
     uint score;             "Score"
     char[1] strand;         "Strand"
     uint thickStart;        "Thick start (same as chromStart)"
     uint thickEnd;          "Thick end (same as chromEnd)"
     uint reserved;          "Item color"
     string svType;          "SV Type|DEL, INS, DUP or INV"
-    int svLen;              "SV Length|Absolute length of the SV in base pairs"
+    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/INV/CPX"
+    int AC;                 "Allele Count|Placeholder (2 * sampleCount); Gustafson callset is site-level"
     uint sampleCount;       "Sample Count|Number of samples carrying this variant (SUPP)"
     uint varCalls;          "Caller Support|Number of per-caller calls supporting this variant"
     uint precise;           "Precise Boundaries|1 if the source caller flagged this variant PRECISE"
     string strands;         "Strands|Strand orientation from the source caller"
     )