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/lrSv1kgOnt.as src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as
index 85ed87eb1db..7b93be43a3d 100644
--- src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as
+++ src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as
@@ -1,29 +1,30 @@
 table lrSv1kgOnt
 "Long-read structural variants from 1000 Genomes ONT"
     (
     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 svClass;     "SV Class|INS, DEL, or COMPLEX"
-    int svLen;          "SV Length|Length of the structural variant in base pairs"
+    string svType;      "SV Type|INS, DEL, or CPX"
+    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|Number of alternate alleles across all samples (-1 if unknown)"
     string insType;     "Insertion/Deletion Type|solo, partnered, orphan, VNTR, PSD, NUMT, DUP, etc."
     string family;      "Transposon Family|Alu, L1, SVA, HERVK, LTR5_Hs, etc."
     float percResolved; "Percent Resolved|Percentage of inserted sequence resolved by SVAN"
     int tsdLen;         "TSD Length|Target site duplication length in base pairs"
     int polyaLen;       "Poly-A Length|Poly-A tail length in base pairs"
     string conformation; "Conformation|Structural conformation of the insertion"
     int rtLen;          "Retrotransposon Length|Length of the retrotransposon portion of the insert"
     int nbMotifs;       "VNTR Motif Count|Number of tandem repeat motifs within a VNTR"
     string srcGene;     "Source Gene|Gene from which a processed pseudogene was retrotransposed"
     int nbExons;        "Retrotransposed Exons|Number of exons retrotransposed (processed pseudogenes)"
     string notCanonical; "Non-canonical MEI|Yes if the mobile element insertion is non-canonical"
-    int alleleCount;    "Allele Count|Number of alternate alleles across all samples (-1 if unknown)"
     int alleleNumber;   "Allele Number|Total number of alleles genotyped (-1 if unknown)"
     float alleleFreq;   "Allele Frequency|Alternate allele frequency across all samples (-1 if unknown)"
     )