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/srSv/onekg3202SrVcfToBed.py src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.py
index 71f0f061da7..b4857eabd8b 100644
--- src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.py
+++ src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.py
@@ -1,32 +1,36 @@
 #!/usr/bin/env python3
 """Convert 1KG 3,202-sample GATK-SV short-read VCF to BED9+.
 
 Short-read comparator track for the lrSv collection.
 
 Source:
     https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz
 Paper:
     Byrska-Bishop et al. 2022, Cell, PMID 36055201.
 
 Usage:
     lrSv1kg3202SrVcfToBed.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
+
 SV_COLORS = {
     "DEL": "200,0,0",      # red
     "INS": "0,0,200",      # blue
     "DUP": "0,160,0",      # green
     "INV": "230,140,0",    # orange
     "CPX": "140,0,200",    # purple
     "CTX": "100,100,100",  # grey
     "CNV": "150,80,0",     # brown
 }
 
 
 def parseInfo(infoStr):
     d = {}
     for item in infoStr.split(";"):
         if "=" in item:
@@ -58,65 +62,79 @@
 def main():
     if len(sys.argv) != 3:
         print(__doc__, file=sys.stderr)
         sys.exit(1)
 
     inPath, outPath = sys.argv[1], sys.argv[2]
     opener = gzip.open if inPath.endswith(".gz") else open
 
     with opener(inPath, "rt") 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]
             filt = fields[6]
             info = parseInfo(fields[7])
 
-            svType = info.get("SVTYPE", ".")
+            svTypeRaw = info.get("SVTYPE", ".")
+            svType = normalizeSvType(svTypeRaw)
             end = int(info.get("END", pos))
-            svLen = abs(toInt(info.get("SVLEN", "0")))
+            srcSvLen = abs(toInt(info.get("SVLEN", "0")))
 
             chromStart = pos - 1
             chromEnd = end
             if chromEnd <= chromStart:
                 chromEnd = chromStart + 1
 
             # Translocations: the END is on chr2; cap the item width to 1 bp
             # on the chromosome-1 side.
             chr2 = info.get("CHR2", "")
             if svType == "CTX" and chr2 and chr2 != chrom:
                 chromEnd = chromStart + 1
 
+            svLen = chromEnd - chromStart
+            if svType in ("INS", "MEI"):
+                insLen = srcSvLen
+            else:
+                insLen = 0
+
             color = SV_COLORS.get(svType, "100,100,100")
 
+            ac = toInt(info.get("AC", "0"))
+            an = toInt(info.get("AN", "0"))
+
+            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(svLen),
-                str(toInt(info.get("AC", "0"))),
-                str(toInt(info.get("AN", "0"))),
+                str(insLen),
+                str(ac),
+                str(an),
                 f"{toFloat(info.get('AF', '0')):.6f}",
                 f"{toFloat(info.get('POPMAX_AF', '0')):.6f}",
                 f"{toFloat(info.get('AFR_AF', '0')):.6f}",
                 f"{toFloat(info.get('AMR_AF', '0')):.6f}",
                 f"{toFloat(info.get('ASN_AF', '0')):.6f}",
                 f"{toFloat(info.get('EUR_AF', '0')):.6f}",
                 f"{toFloat(info.get('SAN_AF', '0')):.6f}",
                 str(toInt(info.get("N_HET", "0"))),
                 str(toInt(info.get("N_HOMALT", "0"))),
                 info.get("ALGORITHMS", ""),
                 info.get("SOURCE", ""),
                 filt,
                 chr2 if svType == "CTX" else "",
             ]
             fOut.write("\t".join(row) + "\n")