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/lrSvChirmade101.as src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as
index fcfa10edcde..fa17781ea2c 100644
--- src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as
+++ src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as
@@ -1,46 +1,48 @@
 table lrSvChirmade101
 "Chirmade 2026 (GWAS SVatalog) long-read structural variants"
     (
     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, inv, or complex"
-    int svLen;                 "SV Length|Absolute length of the SV in base pairs"
+    string svType;             "SV Type|DEL, INS, DUP, INV, or CPX"
+    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 value (-1); Chirmade catalog is site-level without AC"
     uint gcPct;                "GC Content|Percent GC in the SV region"
     string cytoband;           "Cytoband"
     uint geneCount;            "Gene Count|Number of genes overlapping the SV"
     lstring geneNames;         "Overlapping Genes|Comma-separated gene symbols"
     string geneAtStart;        "Gene at Start|Gene at the left breakpoint"
     string geneAtEnd;          "Gene at End|Gene at the right breakpoint"
     lstring exonName;          "Overlapping Exons"
     lstring cdsName;           "Overlapping CDS"
     string darkOverlap;        "Dark Genes Overlap|Percent overlap with 'dark' (low-mappability) genes"
     lstring clinGenHi;         "ClinGen Haploinsufficient|Haploinsufficiency score/evidence per gene"
     lstring clinGenTs;         "ClinGen Triplosensitive|Triplosensitivity score/evidence per gene"
     lstring gnomadLoefUpper;   "gnomAD LOEUF|Observed/expected LoF upper bound per gene"
     lstring gnomadMisUpper;    "gnomAD Mis O/E|Observed/expected missense upper bound per gene"
     lstring gnomadPli;         "gnomAD pLI|Per-gene pLI"
     lstring gnomadPrec;        "gnomAD pRec|Per-gene pRec"
     string repeatPct;          "Repeat Overlap|Percent overlap with repetitive regions"
     string dirtyPct;           "Dirty Region Overlap|Percent overlap with 'dirty' / low-quality regions"
     lstring chrRegion;         "Chromosome Region"
     lstring cgd;               "CGD|Clinical Genomic Database gene annotation"
     lstring omimPheno;         "OMIM Phenotype"
     lstring omimInh;           "OMIM Inheritance"
     lstring clinGenRegion;     "ClinGen Region"
     lstring decipherRegion;    "Decipher Region"
     lstring clinvarVarId;      "ClinVar Variant ID"
     string gnomadAfMax;        "gnomAD AF Max (90% RO)|Max allele frequency across gnomAD populations for overlapping SV"
     string gnomadPopAfMax;     "gnomAD Population AF Max"
     string gnomadHomRefFreq;   "gnomAD Hom/Ref Freq"
     string gnomadHetFreq;      "gnomAD Het Freq"
     string gnomadHomAltFreq;   "gnomAD Hom/Alt Freq"
     string dgvPct;             "DGV Overlap|Percent overlap with Database of Genomic Variants"
     string dgv50ro;            "DGV 50% RO|Matched DGV variant at >=50% reciprocal overlap"
     )