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/lrSvApr.as src/hg/makeDb/scripts/lrSv/lrSvApr.as
index 4b27f3e5bd3..c93e4d5096d 100644
--- src/hg/makeDb/scripts/lrSv/lrSvApr.as
+++ src/hg/makeDb/scripts/lrSv/lrSvApr.as
@@ -1,20 +1,21 @@
 table lrSvApr
 "Arabic Pangenome Reference structural variants, collapsed by graph snarl site"
     (
     string chrom;        "Chromosome"
     uint   chromStart;   "Start position"
     uint   chromEnd;     "End position"
     string name;         "Graph snarl ID (variant site)"
     uint   score;        "Score, 0-1000 (scaled AF)"
     char[1] strand;      "Strand (.)"
     uint   thickStart;   "Thick start"
     uint   thickEnd;     "Thick end"
     uint   itemRgb;      "Color by SV type"
     string svType;       "SV Type|INS, DEL, CPX or MIXED (MIXED = snarl with alts of different classes)"
-    int    svLen;        "SV Length|max |len(ALT) - len(REF)| across alt alleles at this snarl"
+    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 (AC)|sum across all passing alt alleles"
     int    numAlts;      "Number of alt alleles|at this snarl passing the 50bp filter"
-    int    alleleCount;  "Allele Count (AC)|sum across all passing alt alleles"
     int    alleleNumber; "Allele Number (AN)|called alleles at this site (excludes GRCh38 ref column)"
-    float  alleleFreq;   "Allele Frequency (AF)|alleleCount / alleleNumber"
+    float  alleleFreq;   "Allele Frequency (AF)|AC / alleleNumber"
     int    numSamples;   "Samples with data (NS)"
     )