Merge pull request #36 from bacpop/issue35

Addresses issue #35
bacpop · Jul 17, 2024 · eb917a3 · eb917a3
2 parents 27e8a45 + 0f0acd3
commit eb917a3
Showing 1 changed file with 15 additions and 11 deletions.
diff --git a/src/indexing.cpp b/src/indexing.cpp
@@ -458,16 +458,20 @@ void calculate_genome_paths(const std::vector<Kmer>& head_kmer_arr,
                     }
                 }
 
-                // map to last entry and assign end-contig
-                auto um_pair = get_um_data(ccdbg, head_kmer_arr, prev_head);
-                auto& um_data = um_pair.second;
-
-                um_data->set_end_contig(colour_ID, nb_colours);
-
-                // add delimiter between contigs
-                genome_path += contig_path;
-                genome_path += ";";
-                contig_ID++;
+                // in case where whole contig removed, do not add to FM index
+                // otherwise causes out of range error with head_kmer_arr as k-mer not present
+                if (prev_head != 0) {
+                    // map to last entry and assign end-contig
+                    auto um_pair = get_um_data(ccdbg, head_kmer_arr, prev_head);
+                    auto& um_data = um_pair.second;
+
+                    um_data->set_end_contig(colour_ID, nb_colours);
+
+                    // add delimiter between contigs
+                    genome_path += contig_path;
+                    genome_path += ";";
+                    contig_ID++;
+                }
             }
         }
     }
@@ -585,4 +589,4 @@ NodeColourVector index_graph(std::vector<Kmer>& head_kmer_arr,
 
     // return node_colour vector
     return node_colour_vector;
-}
+}