Merge pull request #50 from martinghunt/bug_in_get_one_variant_for_on…

…e_contig_coding

Bug in get one variant for one contig coding

ariba/assembly_variants.py

@@ -64,12 +64,12 @@ def _get_mummer_variants(cls, snp_file):
     def _get_variant_effect(cls, variants, ref_sequence):
         '''variants = list of variants in the same codon.
            returns type of variant (cannot handle more than one indel in the same codon).'''
-        if len(variants) == 0:
-            return None
+        assert len(variants) != 0
 
         var_types = [x.var_type for x in variants]
         if len(set(var_types)) != 1:
-            return None
+            print('More than one type of variant in the same codon not yet implemented!', ref_sequence.id, file=sys.stderr)
+            return 'MULTIPLE', '.', '.'
 
         var_type = var_types[0]
 
@@ -306,7 +306,7 @@ def get_variants(self, ref_sequence_name, nucmer_coords):
 
                     # include new variant, except if the ref type is variants only and
                     # the new variant matches to a known variant
-                    if new_variant is not None and (ref_sequence_type != 'variants_only' or len(new_variant[5]) > 0 or new_variant[3] == 'INDELS'):
+                    if new_variant is not None and (ref_sequence_type != 'variants_only' or len(new_variant[5]) > 0 or new_variant[3] in ['MULTIPLE', 'INDELS']):
                             variants[contig].append(new_variant)
                     used_known_variants.update(used_variants)
 

ariba/samtools_variants.py

@@ -167,7 +167,7 @@ def get_depths_at_position(self, seq_name, position):
         if seq_name in d and position in d[seq_name]:
             return d[seq_name][position]
         else:
-            return None
+            return 'ND', 'ND', 'ND', 'ND'
 
 
     def run(self):

ariba/tests/samtools_variants_test.py

@@ -130,8 +130,8 @@ def test_get_depths_at_position(self):
         samtools_vars.run()
         tests = [
             (('ref', 425), ('C', 'T', 31, '18,13')),
-            (('not_a_ref', 10), None),
-            (('ref', 1000000000), None)
+            (('not_a_ref', 10), ('ND', 'ND', 'ND', 'ND')),
+            (('ref', 1000000000), ('ND', 'ND', 'ND', 'ND'))
         ]
         for (ref, pos), expected in tests:
             got = samtools_vars.get_depths_at_position(ref, pos)