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/lrSvHgsvc3.as src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as
index 00190f98798..b208443e0b2 100644
--- src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as
+++ src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as
@@ -1,26 +1,27 @@
 table lrSvHgsvc3
 "HGSVC3 long-read structural variants (65 samples)"
     (
     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|Number of haplotypes carrying the variant across 65 diploid samples"
+    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|Number of haplotypes carrying the variant across 65 diploid samples"
     uint sampleCount;        "Sample Count|Number of distinct samples carrying the variant (ignoring haplotype suffix)"
     string homRef;           "Reference Homology|Homology (bp) at breakpoints in the reference (5',3'), insdel only"
     string homTig;           "Contig Homology|Homology (bp) at breakpoints in the assembly contig (5',3'), insdel only"
     string regionRefInner;   "Inversion Inner Region|Inner coordinate range of the inversion, INV only"
     string te;               "Transposable Element|TE class of the inserted/deleted sequence, insdel only"
     string refTrf;           "In Tandem Repeat|Variant falls in a reference Tandem Repeat Finder region (True/False)"
     float refSd;             "Segmental Duplication Overlap|Fraction of the variant overlapping reference segmental duplications (0-1)"
     lstring mergeSamples;    "Carrier Haplotypes|Comma-separated list of haplotype IDs carrying this variant"
     string win500;           "Flanking +/- 500 bp|Genomic window around the variant"
     string win2k;            "Flanking +/- 2000 bp|Genomic window around the variant"
     )