hacky attempt for Illumina#65

brentp · May 17, 2021 · cc04f27 · cc04f27
1 parent e805e26
commit cc04f27
Showing 1 changed file with 11 additions and 2 deletions.
diff --git a/src/python/lib/grm/vcfgraph/vcfgraph.py b/src/python/lib/grm/vcfgraph/vcfgraph.py
@@ -174,8 +174,17 @@ def add_record(self, vcf, allele_graph, varId, ins_info_key):
             if "<" in alt:
                 if alt == "<INS>":
                     if ins_info_key not in vcf.info:
-                        raise Exception(
-                            f"Missing key {ins_info_key} for <INS> at {self.chrom}:{vcf.pos}; ")
+                        if "RIGHT_SVINSSEQ" in vcf.info and "LEFT_SVINSSEQ" in vcf.info:
+                            l = vcf.info["LEFT_SVINSSEQ"]
+                            r = vcf.info["RIGHT_SVINSSEQ"]
+                            if isinstance(l, (tuple, list)):
+                                l = l[0]
+                            if isinstance(r, (tuple, list)):
+                                r = r[0]
+                            vcf.info[ins_info_key] = l + ('N' * 200) + r
+                        else:
+                            raise Exception(
+                                f"Missing key {ins_info_key} for <INS> at {self.chrom}:{vcf.pos}; ")
                     ins_seq = vcf.info[ins_info_key].upper()
                     if re.search(r'[^ACGTNXacgtnx]', ins_seq):
                         raise Exception("Illegal character in INS sequence: %s" % ins_seq)