updated logic to deal with erroneous reporting of reference genotype …

…(issue #1)

sonnei_genotype.py

@@ -331,7 +331,15 @@ def parseGeno(this_groups, proportions, group_names):
     if (len(subclades) == 0) and ('3.6' in clades):
         subclades.append('3.6.0')
 
-    # state subclade for reference
+    # if we've removed 2.8.2 but still have no subclades, check that the value in clades is not 2.8
+    # if it ISN'T 2.8, and it's some other clade, then report that clade + .0
+    # if we also don't have a subclade call, report the lineage + .0.0
+    if (len(subclades) == 0) and ('2.8' not in clades):
+        try:
+            subclades.append(clades[0] + '.0')
+        except IndexError:
+            subclades.append(primary[0] + '.0.0')
+    # otherwise if the clade is 2.8, then we indeed do have the reference genotype
     if len(subclades) == 0:
         subclades.append('2.8.2')  # anything with no subclade, and 2.8.2 SNP NOT called, belongs in 2.8.2 with 53G