# Like the naive algorithm but we break out of the inner loop as soon as our
# mismatch budget exceeds the maximum allowed Hamming distance.
def naive_approx_hamming(p, t, maxHammingDistance=1):
occurrences = 
for i in range(0, len(t) - len(p) + 1): # for all alignments
nmm = 0
for j in range(0, len(p)): # for all characters
if t[i+j] != p[j]: # does it match?
nmm += 1 # mismatch
if nmm > maxHammingDistance:
break # exceeded maximum distance
if nmm <= maxHammingDistance:
# approximate match; return pair where first element is the
# offset of the match and second is the Hamming distance