fix ClinVar header #AlleleID + GRCh38 filter (was UnboundLocalError)

- header lstrip # for #AlleleID, init ci_*=None, filter Assembly!=GRCh38
- loaded 3960956 GRCh38 variants (was 0)
- offline now correctly maps P/LP vs VUS

annotate_clean.py

@@ -389,27 +389,32 @@ def _load_clinvar(clinvar_path):
         opener = gzip.open if str(clinvar_path).endswith(".gz") else open
         with opener(clinvar_path, "rt") as fh:
             header = None
+            ci_chr = ci_start = ci_ref = ci_alt = ci_sig = ci_asm = None
             for line in fh:
                 if line.startswith("#"):
+                    if header is None and line.lstrip("#").startswith("AlleleID"):
+                        line = line.lstrip("#")
+                    else:
                         continue
                 if header is None:
                     header = line.rstrip("\n").split("\t")
-                    # Find column indices
                     try:
                         ci_chr = header.index("Chromosome")
                         ci_start = header.index("Start")
                         ci_ref = header.index("ReferenceAllele")
                         ci_alt = header.index("AlternateAllele")
                         ci_sig = header.index("ClinicalSignificance")
+                        ci_asm = header.index("Assembly") if "Assembly" in header else None
                     except ValueError:
-                        # Fallback for older format: try different names
+                        header = None
                         continue
                     continue
                 parts = line.rstrip("\n").split("\t")
                 if len(parts) <= max(ci_chr, ci_start, ci_ref, ci_alt, ci_sig):
                     continue
+                if ci_asm is not None and parts[ci_asm] != "GRCh38":
+                    continue
                 chrom = parts[ci_chr]
-                # ClinVar Chromosome is 1,2.. not chr1
                 chrom_norm = f"chr{chrom}" if not chrom.startswith("chr") else chrom
                 try:
                     pos = int(parts[ci_start])
@@ -417,9 +422,6 @@ def _load_clinvar(clinvar_path):
                     continue
                 ref = parts[ci_ref]; alt = parts[ci_alt]
                 sig = parts[ci_sig]
-                # Normalize significance to ACMG
-                # ClinVar: Pathogenic, Likely pathogenic, Uncertain significance, Likely benign, Benign, etc.
-                # Map to our 5-tier
                 sig_lower = sig.lower()
                 if "pathogenic" in sig_lower and "likely" not in sig_lower:
                     acmg = "Pathogenic"
@@ -432,7 +434,6 @@ def _load_clinvar(clinvar_path):
                 else:
                     acmg = "Uncertain significance"
                 key = (chrom_norm, pos, ref, alt)
-                # Also add without chr prefix for matching
                 key2 = (chrom, pos, ref, alt)
                 m[key] = acmg
                 m[key2] = acmg