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/abelSvVcfToBed.py src/hg/makeDb/scripts/srSv/abelSvVcfToBed.py
index 1869080093e..d54cb5bbd74 100755
--- src/hg/makeDb/scripts/srSv/abelSvVcfToBed.py
+++ src/hg/makeDb/scripts/srSv/abelSvVcfToBed.py
@@ -1,30 +1,35 @@
 #!/usr/bin/env python3
 """Convert an Abel et al. 2020 CCDG structural-variant VCF (Build38 or Build37)
 to the bed14+ representation used by the abelSv track.
 
 Inputs: gzipped VCF on stdin (pass through zcat).
 Output: tab-separated bed rows on stdout.
 
 Usage:
     zcat Build38.public.v2.vcf.gz | vcfToBed.py B38 > B38.bed
     zcat Build37.public.v2.vcf.gz | vcfToBed.py B37 > B37.prelift.bed
 """
 import sys
 import gzip
+import os
 import re
 
+# Share the lrSv svName/normalizeSvType helpers without duplicating the module.
+sys.path.insert(0, os.path.expanduser("~/kent/src/hg/makeDb/scripts/lrSv"))
+from lrSvCommon import svName, normalizeSvType
+
 # RGB colors per SV type (flat solid colors)
 COLORS = {
     "DEL": "220,50,32",    # red
     "DUP": "0,120,200",    # blue
     "INV": "230,140,0",    # orange
     "MEI": "140,80,180",   # purple
     "BND": "120,120,120",  # grey
 }
 
 # Population codes present in INFO (per-ancestry AC/AN)
 POPS = ["AFR", "AMR", "NFE", "FE", "EAS", "SAS", "PI", "Other"]
 
 # Integer fields we extract and report as int
 INT_FIELDS = ["AC", "AN", "NSAMP", "NFAM"]
 FLOAT_FIELDS = ["MSQ", "AF"]
@@ -97,30 +102,33 @@
         chrom, pos, vid, ref, alt, qual, filt, info = f[:8]
         info_d = parse_info(info)
 
         # Skip secondary BND records; we keep only the primary.
         if info_d.get("SECONDARY"):
             continue
 
         svtype_raw = info_d.get("SVTYPE", "")
         # Also check ALT for richer subtype info
         alt_sv = get_alt_svtype(alt)
         svclass = classify_svtype(alt_sv or svtype_raw)
 
         if svclass not in COLORS:
             continue  # skip unknown types
 
+        # Canonicalize via lrSvCommon (DEL/DUP/INV/MEI/BND are already canonical).
+        svType = normalizeSvType(svclass)
+
         start = int(pos) - 1  # VCF is 1-based
         mate_chrom = ""
         mate_pos = -1
         sv_length = -1
         end = start + 1  # default single-width
 
         if svclass == "BND":
             mate_chrom, mate_pos = parse_bnd_alt(alt)
             if add_chr and mate_chrom and not mate_chrom.startswith("chr"):
                 mate_chrom = "chr" + mate_chrom
             end = start + 1
         else:
             if "END" in info_d:
                 end = int(info_d["END"])
             if "SVLEN" in info_d:
@@ -150,43 +158,65 @@
         except ValueError:
             msq = 0.0
         nsamp = int(info_d.get("NSAMP", "0"))
         nfam = int(info_d.get("NFAM", "0"))
 
         # Score for bigBed: scale AF to 0-1000
         score = min(1000, max(0, int(round(af * 1000))))
 
         # Per-population AC/AN (missing -> 0)
         pop_vals = []
         for pop in POPS:
             pop_ac = int(info_d.get(f"AC_{pop}", "0").split(",")[0])
             pop_an = int(info_d.get(f"AN_{pop}", "0"))
             pop_vals.append((pop_ac, pop_an))
 
+        # svLen canonical = reference span; keep legacy abs(SVLEN) as the displayed
+        # length too by writing it into svLen when non-BND (matches legacy abelSv
+        # filter range). For BND, use -1 (a sentinel preserved in the as schema).
+        if svclass == "BND":
+            svLen = -1
+            insLen = 0
+        else:
+            svLen = end - start
+            if svclass == "MEI":
+                # For MEI, abs(SVLEN) is the inserted-element size.
+                # abelSv VCF reports MEI with negative SVLEN (e.g. -303),
+                # so test != 0 rather than > 0.
+                insLen = abs(sv_length) if sv_length != 0 and sv_length != -1 else 0
+            else:
+                insLen = 0
+
         rgb = COLORS[svclass]
+
+        featLen = insLen if svType in ("INS", "MEI") else (svLen if svLen > 0 else None)
+        name = svName(svType, featLen, ac)
+
         row = [
             chrom, str(start), str(end),
-            vid,
+            name,
             str(score),
             ".",
             str(start), str(end),
             rgb,
-            svclass,
-            str(sv_length),
+            svType,
+            str(svLen),
+            str(insLen),
+            str(ac),
             out_tag,
             filt,
-            str(ac), str(an),
+            str(an),
             f"{af:.6f}",
             f"{msq:.2f}",
             str(nsamp), str(nfam),
             mate_chrom, str(mate_pos),
         ]
         # Append per-pop AC/AN in the order: AFR, AMR, NFE, FE, EAS, SAS, PI, Other
         for ac_p, an_p in pop_vals:
             row.append(str(ac_p))
             row.append(str(an_p))
 
         print("\t".join(row))
 
 
 if __name__ == "__main__":
     main()