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/lrSvKwanho.as src/hg/makeDb/scripts/lrSv/lrSvKwanho.as
index 8a490015eb6..e14247413bb 100644
--- src/hg/makeDb/scripts/lrSv/lrSvKwanho.as
+++ src/hg/makeDb/scripts/lrSv/lrSvKwanho.as
@@ -1,42 +1,44 @@
 table lrSvKwanho
 "Kim 2026 Parkinson's disease brain 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 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|Total AC across PD+HC+ILBD cohorts"
     string sizeBin;             "Size Bin|Length category used in the paper (e.g. [50,100))"
     uint qual;                  "Quality|Variant quality score from the joint callset"
     uint supp;                  "Caller Support|Number of SV callers supporting this variant"
     string suppVec;             "Cohort Support Vector|Bitmask indicating which cohorts carry the variant (PD/ILBD/HC)"
     float missingRate;          "Missing-genotype Rate|Fraction of samples with missing genotype at this site"
     float caseRate;             "Case Carrier Rate|Fraction of PD+ILBD cases carrying the variant"
     float controlRate;          "Control Carrier Rate|Fraction of HC controls carrying the variant"
     float differentialRate;     "Case-Control Differential|caseRate - controlRate (negative: enriched in controls)"
     float afPd;                 "Allele Frequency (PD)|Alternate allele frequency in Parkinson's disease samples"
     float afHc;                 "Allele Frequency (HC)|Alternate allele frequency in healthy-control samples"
     float afIlbd;               "Allele Frequency (ILBD)|Alternate allele frequency in incidental Lewy body disease samples"
     uint acPd;                  "Allele Count (PD)|Alternate allele count in PD samples"
     uint acHc;                  "Allele Count (HC)|Alternate allele count in HC samples"
     uint acIlbd;                "Allele Count (ILBD)|Alternate allele count in ILBD samples"
     uint anPd;                  "Allele Number (PD)|Total called alleles in PD samples"
     uint anHc;                  "Allele Number (HC)|Total called alleles in HC samples"
     uint anIlbd;                "Allele Number (ILBD)|Total called alleles in ILBD samples"
     uint nCarriersPd;           "Carrier Count (PD)"
     uint nCarriersHc;           "Carrier Count (HC)"
     uint nCarriersIlbd;         "Carrier Count (ILBD)"
     uint ldSnpsCount;           "LD SNPs|Number of nearby SNPs in linkage disequilibrium with this SV"
     uint totalSnpsNearby;       "Nearby SNPs|Total number of SNPs in the surrounding window"
     float avgMapQuality;        "Avg Mapping Quality|Average read mapping quality at the SV"
     float avgReadsPerSample;    "Avg Reads / Sample|Average supporting reads per sample"
     lstring pdCarriers;         "PD Carriers|Sample IDs of PD carriers"
     lstring hcCarriers;         "HC Carriers|Sample IDs of HC carriers"
     lstring ilbdCarriers;       "ILBD Carriers|Sample IDs of ILBD carriers"
     )