match dsODN sequences

[YichaoOU]

Is your feature request related to a problem? Please describe.
Current dsODN sequence matching doesn't allow mismatches
df_alleles["Aligned_Sequence"].str.find(args.dsODN) > 0

Describe the solution you'd like
we could just do a from skbio.alignment import StripedSmithWaterman to match dsODN.

Yichao

[kclem]

Would you also allow gaps? And how many mismatches?

[YichaoOU]

For the 34bp dsODN sequence, we use a score cutoff of 30, which could potentially allow up to 7 mismatches or a short gap.

for StripedSmithWaterman, a match is +2 and a mismatch is -3.

<style> </style>

#Match	#Mis-Match	Score
34	0	68
33	1	63
32	2	58
31	3	53
30	4	48
29	5	43
28	6	38
27	7	33
26	8	28
25	9	23