Merge pull request #18 from bcgsc/region_coord

ntjoin_assemble.py: Fix off-by-one error with output scaffolds
bcgsc · Jan 31, 2020 · a8e0f07 · a8e0f07
2 parents 144fe44 + e81c2ff
commit a8e0f07
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/bin/ntjoin_assemble.py b/bin/ntjoin_assemble.py
@@ -481,9 +481,9 @@ def reverse_complement(sequence):
     def get_fasta_segment(path_node, sequence):
         "Given a PathNode and the contig sequence, return the corresponding sequence"
         if path_node.ori == "-":
-            return Ntjoin.reverse_complement(sequence[path_node.start:path_node.end+1]) + \
+            return Ntjoin.reverse_complement(sequence[path_node.start:path_node.end]) + \
                    "N"*path_node.gap_size
-        return sequence[path_node.start:path_node.end+1] + "N"*path_node.gap_size
+        return sequence[path_node.start:path_node.end] + "N"*path_node.gap_size
 
     @staticmethod
     def format_bedtools_genome(scaffolds):