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/lrSvGustafsonVcfToBed.py src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py
index 43e9fbfd1a0..f2879004f6b 100644
--- src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py
@@ -1,114 +1,130 @@
 #!/usr/bin/env python3
 """Convert the Gustafson 2024 1000G ONT Jasmine-merged SV VCF to BED9+.
 
 Usage:
     lrSvGustafsonVcfToBed.py input.vcf.gz output.bed
 
 Source:
     https://s3.amazonaws.com/1000g-ont/Gustafson_etal_2024_preprint_SUPPLEMENTAL/
     20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz
 Paper:
     Gustafson et al. 2024, bioRxiv / Genome Res, PMID 39358015.
 """
 
 import gzip
-import subprocess
+import os
 import sys
 
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+from lrSvCommon import svName, normalizeSvType
+
 SV_COLORS = {
     "DEL": "200,0,0",      # red
     "INS": "0,0,200",      # blue
     "DUP": "0,160,0",      # green
     "INV": "230,140,0",    # orange
 }
 
 # Jasmine END on chrM can overshoot by one base; clip to chrM length.
 CHRM_LEN = 16569
 
 
 def openVcf(path):
     """Open a local .vcf.gz via gzip; everything else as plain text."""
     return gzip.open(path, "rt") if path.endswith(".gz") else open(path, "rt")
 
 
 def parseInfo(infoStr):
     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)
 
     inPath, outPath = sys.argv[1], sys.argv[2]
 
-    # bcftools view -H strips the header so we don't have to; but gzip is fine
-    # for this file and saves the external dependency.
     with openVcf(inPath) as fIn, open(outPath, "w") as fOut:
         for line in fIn:
             if line.startswith("#"):
                 continue
             fields = line.rstrip("\n").split("\t")
             chrom = fields[0]
             pos = int(fields[1])
-            name = fields[2]
+            rowName = fields[2]
             info = parseInfo(fields[7])
 
-            svType = info.get("SVTYPE", ".")
+            svTypeRaw = info.get("SVTYPE", ".")
+            svType = normalizeSvType(svTypeRaw)
             end = int(info.get("END", pos))
             try:
-                svLen = int(float(info.get("SVLEN", "0")))
+                svLenRaw = int(float(info.get("SVLEN", "0")))
             except ValueError:
-                svLen = 0
+                svLenRaw = 0
             try:
                 supp = int(info.get("SUPP", "0"))
             except ValueError:
                 supp = 0
             try:
                 varCalls = int(info.get("VARCALLS", "0"))
             except ValueError:
                 varCalls = 0
             precise = 1 if "PRECISE" in info else 0
             strands = info.get("STRANDS", "")
             if strands == "??":
                 strands = ""
 
             chromStart = pos - 1
             chromEnd = end
             if chromEnd <= chromStart:
                 chromEnd = chromStart + 1
             if chrom == "chrM" and chromEnd > CHRM_LEN:
                 chromEnd = CHRM_LEN
 
-            absSvLen = abs(svLen)
+            svLen = chromEnd - chromStart
+            if svType in ("INS", "MEI"):
+                insLen = abs(svLenRaw)
+            else:
+                insLen = 0
+
+            # Gustafson callset is site-level without AC; 2 * SUPP
+            # is the diploid carrier upper bound.
+            ac = supp * 2
+
             color = SV_COLORS.get(svType, "100,100,100")
 
+            featLen = insLen if svType in ("INS", "MEI") else svLen
+            name = svName(svType, featLen, ac)
+
             row = [
                 chrom,
                 str(chromStart),
                 str(chromEnd),
                 name,
                 "0",
                 ".",
                 str(chromStart),
                 str(chromEnd),
                 color,
                 svType,
-                str(absSvLen),
+                str(svLen),
+                str(insLen),
+                str(ac),
                 str(supp),
                 str(varCalls),
                 str(precise),
                 strands,
             ]
             fOut.write("\t".join(row) + "\n")
 
 
 if __name__ == "__main__":
     main()