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Error when query or target is the empty string and task='path' #191

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RubenBSB opened this issue Oct 6, 2021 · 0 comments
Open

Error when query or target is the empty string and task='path' #191

RubenBSB opened this issue Oct 6, 2021 · 0 comments
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@RubenBSB
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RubenBSB commented Oct 6, 2021

Description
When using edlib.align with an empty query and task='path', the cigar is 'None'.

To Reproduce

result = edlib.align("", "abc", task="path")
edlib.getNiceAlignment(result, "", "abc")

This raises the following error :

Exception: The object alignResult contains an empty CIGAR string. Users must run align() with task='path'. Please check the input alignResult

Expected behavior
In my opinion, the cigar should indicate 3 deletions from the target in this case :

cigar = 3D

Environment

  • Python 3.9.6
  • edlib version 1.3.9
@RubenBSB RubenBSB added the bug label Oct 6, 2021
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