Fix for vcf_new when alignment doesn't have a const site of a certain base
@@ -554,6 +554,8 @@ class TreeAnc(object):
alignment_patterns_const = {}
for base in states:
p = base*nseq
+ #if the alignment doesn't have a const site of this base, don't add! (ex: no '----' site!)
+ if len(np.where(refMod==base)[0]):
alignment_patterns_const[p] = [len(reduced_alignment_const),
list(np.where(refMod==base)[0])]
reduced_alignment_const.append(list(p))
