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Cigar results interpretation #203

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luchaoqi opened this issue Mar 22, 2022 · 0 comments
Open

Cigar results interpretation #203

luchaoqi opened this issue Mar 22, 2022 · 0 comments
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@luchaoqi
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Hello, thanks for this awesome and fast tool! I am new to edlib and would like to understand alignment results better as I didn't find a good example here

To Reproduce

import edlib
query = 'AAGGATTACT' # ligation barcode
target = 'AAGGATTACNT' # read sequence - I added a 'N' at the end before 'T'
edlib.align(query, target, mode='SHW', task='path')

Results

{'editDistance': 1, 'alphabetLength': 5, 'locations': [(0, 8), (0, 9), (0, 10)], 'cigar': '9=1I'}

Expected behavior

The above results show three end locations and I assume they are in deletion, mismatch, and insertion order. But the cigar results only show the case for insertion.
In my real-world problem, the mismatches are having more chances than indels. So is there any plan to solve this problem or did I miss any information to achieve this?

Environment (please complete the following information):

  • OS: Debian
  • Version Python 3.7.12
% pip show edlib
Name: edlib
Version: 1.3.9
@luchaoqi luchaoqi added the bug label Mar 22, 2022
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