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/lrSvAou1k.as src/hg/makeDb/scripts/lrSv/lrSvAou1k.as
index beb1cf957ee..99edaee20b0 100644
--- src/hg/makeDb/scripts/lrSv/lrSvAou1k.as
+++ src/hg/makeDb/scripts/lrSv/lrSvAou1k.as
@@ -1,33 +1,35 @@
 table lrSvAou1k
 "All of Us long-read structural variants"
     (
     string chrom;           "Chromosome"
     uint chromStart;        "Start position"
     uint chromEnd;          "End position"
     string name;            "Variant Name"
     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 or INS"
-    int svLen;              "SV Length|Length of the structural variant in base pairs"
+    int svLen;              "SV Length|Length of the structural variant on the reference in base pairs"
+    int insLen;             "Insertion Length|Length of inserted sequence, 0 for DEL/INV/CPX"
+    int AC;                 "Allele Count|Approximate allele count (5008 * max population AF; AoU site-level data does not publish AC directly)"
     float afAfr;            "AF African|Allele frequency in African/African American samples"
     float afAmr;            "AF Admixed American|Allele frequency in Admixed American samples"
     float afEas;            "AF East Asian|Allele frequency in East Asian samples"
     float afEur;            "AF European|Allele frequency in European samples"
     float afSas;            "AF South Asian|Allele frequency in South Asian samples"
     string fst;             "Fst (AFR vs Non-AFR)|Fixation index between African and non-African populations"
     lstring omimGenes;      "OMIM Genes|OMIM genes intersected with pLI and LOEUF scores"
     lstring diseaseGenes;   "Disease Genes|Disease genes intersected with pLI and LOEUF scores"
     lstring cancerGenes;    "Cancer Genes|Cancer genes intersected with pLI and LOEUF scores"
     lstring acmgGenes;      "ACMG Genes|ACMG genes intersected with pLI and LOEUF scores"
     string regElement;      "Regulatory Element|Type of regulatory element intersected (e.g. enhancer, promoter)"
     string segDup;          "SegDup|Segmental duplication association (INS: within 1kb, DEL: intersect)"
     string tandemRepeat;    "Tandem Repeat|Tandem repeat intersected"
     string otherLrDatasets; "Other LR Datasets|Detected in other long-read datasets (HPRC, HGSVC, 1KG-ONT)"
     string detectedInSr;    "Detected in SR|Detected in matched AoU short-read data"
     lstring eqtls;          "eQTLs|eQTL associations: gene(qvalue)"
     lstring gwas;           "GWAS Associations|GWAS associations: trait(gene, rsID, pvalue, LD_r2)"
     lstring traitAssoc;     "SV-Trait Associations|SV-trait associations in AoU Phase I (Carrier%, Non-carrier%, OR, 95% CI, pvalue)"
     )