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/lrSvHgsvc2.as src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as
index 24578a4dda4..33ed8694100 100644
--- src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as
+++ src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as
@@ -1,30 +1,31 @@
 table lrSvHgsvc2
 "HGSVC2 long-read structural variants (32 haplotype-resolved genomes)"
     (
     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, or INV"
-    int svLen;                 "SV Length|Absolute length of the SV in base pairs"
-    uint alleleCount;          "Allele Count|MERGE_AC - carrier-haplotype count from the callerset merge"
+    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|MERGE_AC - carrier-haplotype count from the callerset merge"
     uint sampleCount;          "Sample Count|Distinct samples carrying the variant (ignoring haplotype suffix)"
     string cytoband;           "Cytoband (BAND)"
     float refSd;               "Segmental Duplication|Fraction of variant overlapping reference segmental duplications"
     string refTrf;             "In Tandem Repeat|Whether the variant falls in a Tandem Repeat Finder region (True/False)"
     uint refseqCds;            "RefSeq CDS Overlap|Base pairs overlapping CDS"
     uint refseqUtr3;           "RefSeq 3' UTR Overlap"
     uint refseqUtr5;           "RefSeq 5' UTR Overlap"
     uint refseqIntron;         "RefSeq Intron Overlap"
     uint refseqNcrna;          "RefSeq ncRNA Overlap"
     uint refseqUp5k;           "RefSeq +/- 5kb Upstream"
     uint refseqDn5k;           "RefSeq +/- 5kb Downstream"
     string pliMax;             "Max gnomAD pLI|Max pLI of genes overlapping this SV"
     string loeufMin;           "Min gnomAD LOEUF|Minimum LOEUF upper bound of overlapping genes"
     string popAllAf;           "Allele Frequency (all)|Population-level AF (insdel only)"
     string popAfrAf;           "AF African (insdel only)"