Merge pull request #946 from broadinstitute/ct-empty-barcodes

add guardrails for the case where observed barcodes are null
broadinstitute · Apr 10, 2019 · 9254e14 · 9254e14
2 parents 27c36ee + 4cdb643
commit 9254e14
Showing 1 changed file with 7 additions and 6 deletions.
diff --git a/util/illumina_indices.py b/util/illumina_indices.py
@@ -1803,12 +1803,13 @@ def guess_barcodes_for_sample(self, sample_name):
  out_dict["match_type"] = "high_count_novel_pair"
  break
 
- out_dict["guessed_barcode_1"] = putative_match[0]
- out_dict["guessed_barcode_1_name"] = self.barcode_name_map[putative_match[0]]
- if is_dual_index:
- out_dict["guessed_barcode_2"] = putative_match[1]
- out_dict["guessed_barcode_2_name"] = self.barcode_name_map[putative_match[1]]
- out_dict["guessed_barcodes_read_count"] = self.barcodes_seen[(putative_match[0],putative_match[1])]
+ if putative_match[0]!=None:
+ out_dict["guessed_barcode_1"] = putative_match[0]
+ out_dict["guessed_barcode_1_name"] = self.barcode_name_map[putative_match[0]]
+ if is_dual_index and putative_match[1] != None:
+ out_dict["guessed_barcode_2"] = putative_match[1]
+ out_dict["guessed_barcode_2_name"] = self.barcode_name_map[putative_match[1]]
+ out_dict["guessed_barcodes_read_count"] = self.barcodes_seen[(putative_match[0],putative_match[1])]
 
  return out_dict