#506 - vcf allows for unknown QUAL field

src/sniffles/sv.py

@@ -309,7 +309,7 @@ def call(self, config, task) -> Optional[SVCall]:
                         id=f"{first_cand.svtype}.{task.sv_id:X}M{task.id:X}",
                         ref="N",
                         alt=svcall_alt,
-                        qual=round(util.mean(int(cand.qual) for cand in self.candidates)),
+                        qual=util.mean_or_none_round(int(cand.qual) for cand in self.candidates if cand.qual is not None),
                         filter="PASS" if n_samples != 1 else first_cand.filter,
                         info=dict() if n_samples != 1 else first_cand.info,
                         svtype=first_cand.svtype,

src/sniffles/vcf.py

@@ -292,10 +292,10 @@ def write_call(self, call):
                     elif call.svtype == 'BND' and call.alt != '<BND>':
                         call.alt = (call.ref + call.alt[1:]) if call.alt.startswith('N') else call.alt[:-1] + call.ref
 
-        call.qual = max(0, min(60, call.qual))
+        call.qual = max(0, min(60, call.qual)) if call.qual is not None else None
 
         self.write_raw("\t".join(str(v) for v in [call.contig, pos, self.config.id_prefix + call.id, call.ref,
-                                                  call.alt, call.qual, call.filter, info_str, self.genotype_format] +
+                                                  call.alt, call.qual if call.qual is not None else '.', call.filter, info_str, self.genotype_format] +
                                  sample_genotypes))
         self.call_count += 1
 
@@ -325,7 +325,7 @@ def read_svs_iter(self):
                                  id=line_index,
                                  ref=REF,
                                  alt=ALT,
-                                 qual=int(QUAL),
+                                 qual=int(QUAL) if QUAL != '.' else None,
                                  filter=FILTER,
                                  info=info_dict,
                                  svtype=None,