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/lrSvCpc1VcfToBed.py src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py
index 13f01328ff0..277bc06d601 100755
--- src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py
@@ -15,43 +15,48 @@
 Pipeline:
   1. Parse the #CHROM header to identify the 58 CPC sample column indices
      by prefix (HIFI032* or RY*).
   2. Strip the "CHM13v2." contig prefix for hs1 chrom names.
   3. For each VCF row, read the GT field for each CPC sample and compute
      CPC-only AC (count of "1" alleles), AN (count of non-missing alleles),
      and NS (CPC samples with at least one called allele).
   4. Classify each alt allele by length delta d = len(ALT)-len(REF):
          d >= +50   -> INS
          d <= -50   -> DEL
          |d| < 50 and max(len) >= 50 -> CPX
          otherwise  -> dropped (below 50bp threshold)
   5. Drop rows where CPC AC == 0 (HPRC-specific alts).
   6. Collapse all remaining alts sharing the same snarl ID into one output row:
          svType = that class if all alts agree, else MIXED
-         svLen  = max |d| across alts
-         alleleCount = sum of per-alt CPC AC
+         svLen  = reference span (chromEnd - chromStart)
+         insLen = max inserted-sequence length for INS alts (0 otherwise)
+         AC     = sum of per-alt CPC AC
          alleleNumber = CPC AN
-         alleleFreq   = alleleCount / alleleNumber
+         alleleFreq   = AC / alleleNumber
          numSamples   = CPC NS
 
 Usage:
     lrSvCpc1VcfToBed.py input.vcf.gz output.bed chrom.sizes
 """
 
 import gzip
+import os
 import sys
 
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+from lrSvCommon import svName, normalizeSvType
+
 # Colors per SV type
 COLORS = {
     "INS": "0,0,200",       # blue
     "DEL": "200,0,0",       # red
     "CPX": "230,140,0",     # orange
     "MIXED": "120,120,120", # grey
 }
 
 SIZE_THRESHOLD = 50
 
 
 def is_cpc_sample(name):
     """CPC samples are HIFI032* (Chinese, 47) and RY* (Chinese, 11)."""
     return name.startswith("HIFI032") or name.startswith("RY")
 
@@ -78,47 +83,53 @@
         for a in gt.replace("/", "|").split("|"):
             if a == ".":
                 continue
             an += 1
             has_called = True
             if a == "1":
                 ac += 1
         if has_called:
             ns += 1
     return ac, an, ns
 
 
 def emit(site, fout):
     classes = site["types"]
     sv_type = next(iter(classes)) if len(classes) == 1 else "MIXED"
-    rgb = COLORS[sv_type]
+    sv_type = normalizeSvType(sv_type)
+    rgb = COLORS.get(sv_type, "120,120,120")
     chrom = site["chrom"]
     start = site["pos0"]
     end = start + max(site["ref_len"], 1)
     af = (site["ac_sum"] / site["an"]) if site["an"] else 0.0
     score = min(1000, max(0, int(round(af * 1000))))
+    svLen = end - start
+    insLen = site["max_ins"] if sv_type == "INS" else 0
+    featLen = insLen if sv_type in ("INS", "MEI") else svLen
+    name = svName(sv_type, featLen, site["ac_sum"])
     row = [
         chrom, str(start), str(end),
-        site["name"],
+        name,
         str(score),
         ".",
         str(start), str(end),
         rgb,
         sv_type,
-        str(site["svlen"]),
-        str(site["num_alts"]),
+        str(svLen),
+        str(insLen),
         str(site["ac_sum"]),
+        str(site["num_alts"]),
         str(site["an"]),
         f"{af:.6f}",
         str(site["ns"]),
     ]
     fout.write("\t".join(row) + "\n")
 
 
 def main():
     if len(sys.argv) < 4:
         sys.exit("usage: lrSvCpc1VcfToBed.py input.vcf.gz output.bed chrom.sizes")
     in_file = sys.argv[1]
     out_file = sys.argv[2]
     sizes_file = sys.argv[3]
 
     chrom_sizes = {}
@@ -184,40 +195,45 @@
                 continue
 
             pos0 = int(pos) - 1
             key = (chrom, pos0, vid)
             if key != prev_key:
                 if site is not None:
                     emit(site, fout)
                     flushed_sites += 1
                 site = {
                     "chrom": chrom,
                     "pos0": pos0,
                     "ref_len": ref_len,
                     "name": vid,
                     "types": set(),
                     "svlen": 0,
+                    "max_ins": 0,
                     "num_alts": 0,
                     "ac_sum": 0,
                     "an": an,
                     "ns": ns,
                 }
                 prev_key = key
 
             site["types"].add(sv_type)
             if mag > site["svlen"]:
                 site["svlen"] = mag
+            if sv_type == "INS":
+                d = alt_len - ref_len
+                if d > site["max_ins"]:
+                    site["max_ins"] = d
             site["num_alts"] += 1
             site["ac_sum"] += ac
             if an > site["an"]:
                 site["an"] = an
             if ns > site["ns"]:
                 site["ns"] = ns
             kept_rows += 1
 
         if site is not None:
             emit(site, fout)
             flushed_sites += 1
 
     print(f"kept alt rows (CPC carrier):   {kept_rows}", file=sys.stderr)
     print(f"dropped no CPC carrier:        {dropped_no_cpc_carrier}", file=sys.stderr)
     print(f"dropped <{SIZE_THRESHOLD}bp alt rows: {dropped_small}", file=sys.stderr)