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/lrSvTommoJpVcfToBed.py src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py
index f5b7cbd5a67..99eac516c8a 100644
--- src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py
@@ -1,126 +1,137 @@
 #!/usr/bin/env python3
 """Convert ToMMo JSV1 SURVIVOR-merged SV VCF to BED9+ for bigBed.
 
 Usage:
     lrSvTommoJpVcfToBed.py input.vcf.gz output.bed
 """
 
 import gzip
+import os
 import sys
 
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+from lrSvCommon import svName, normalizeSvType
+
 # Colors by SV type (R,G,B)
 SV_COLORS = {
     "DEL": "200,0,0",      # red
     "INS": "0,0,200",      # blue
 }
 
 def parseInfo(infoStr):
     """Parse INFO field into a dict."""
     d = {}
     for item in infoStr.split(";"):
         if "=" in item:
             k, v = item.split("=", 1)
             d[k] = v
         else:
             d[item] = True
     return d
 
 def main():
     if len(sys.argv) != 3:
         print(__doc__, file=sys.stderr)
         sys.exit(1)
 
     inFile, outFile = sys.argv[1], sys.argv[2]
     opener = gzip.open if inFile.endswith(".gz") else open
 
     with opener(inFile, "rt") as fIn, open(outFile, "w") as fOut:
         for line in fIn:
             if line.startswith("#"):
                 continue
 
             fields = line.rstrip("\n").split("\t")
             chrom = fields[0]
             pos = int(fields[1])
             qual = fields[5]
             info = parseInfo(fields[7])
 
-            svType = info.get("SVTYPE", ".")
+            svTypeRaw = info.get("SVTYPE", ".")
+            svType = normalizeSvType(svTypeRaw)
             end = int(info.get("END", pos))
-            svLen = int(float(info.get("SVLEN", "0")))
+            svLenRaw = int(float(info.get("SVLEN", "0")))  # VCF SVLEN for INS
             af = info.get("AF", "0")
             ac = int(info.get("AC", "0"))
             an = int(info.get("AN", "0"))
 
             # Mendelian error fields
             errRatio = info.get("ERROR_FAMILY_RATIO", ".")
             errNum = info.get("ERROR_FAMILY_NUM", "0")
             famNum = info.get("FAMILY_NUM", "0")
 
             # Handle nan/missing AF
             try:
                 afFloat = float(af)
             except ValueError:
                 afFloat = 0.0
 
             # BED is 0-based half-open
             chromStart = pos - 1
 
             # For INS, END == POS so the item has zero width; expand by 1 bp
             chromEnd = end
             if chromEnd <= chromStart:
                 chromEnd = chromStart + 1
 
-            # Absolute SV length
-            absSvLen = abs(svLen)
-
-            # Readable name
-            name = f"{svType} {absSvLen}bp"
+            # svLen = reference span
+            svLen = chromEnd - chromStart
+            # insLen = size of inserted sequence (from SVLEN for INS)
+            if svType in ("INS", "MEI"):
+                insLen = abs(svLenRaw)
+            else:
+                insLen = 0
 
             # Score: map QUAL to 0-1000
             try:
                 score = min(int(round(float(qual) * 2)), 1000)
             except ValueError:
                 score = 0
 
             strand = "."
             color = SV_COLORS.get(svType, "100,100,100")
 
             # Handle missing error ratio
             try:
                 errRatioFloat = float(errRatio)
             except ValueError:
                 errRatioFloat = 0.0
 
             try:
                 errNumInt = int(errNum)
             except ValueError:
                 errNumInt = 0
 
             try:
                 famNumInt = int(famNum)
             except ValueError:
                 famNumInt = 0
 
+            featLen = insLen if svType in ("INS", "MEI") else svLen
+            name = svName(svType, featLen, ac)
+
             row = [
                 chrom,
                 str(chromStart),
                 str(chromEnd),
                 name,
                 str(score),
                 strand,
                 str(chromStart),   # thickStart
                 str(chromEnd),     # thickEnd
                 color,
                 svType,
-                str(absSvLen),
-                f"{afFloat:.6f}",
+                str(svLen),
+                str(insLen),
                 str(ac),
+                f"{afFloat:.6f}",
                 str(an),
                 f"{errRatioFloat:.3f}",
                 str(errNumInt),
                 str(famNumInt),
             ]
             fOut.write("\t".join(row) + "\n")
 
 if __name__ == "__main__":
     main()