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mgatk-del for other species: array length error #96

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clee700 opened this issue Aug 6, 2024 · 1 comment
Open

mgatk-del for other species: array length error #96

clee700 opened this issue Aug 6, 2024 · 1 comment

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@clee700
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clee700 commented Aug 6, 2024

Hello! Thank you for making such a useful tool!

I am reaching out about an issue when using mgatk-del for other species. In the clifind.py file (mgatk--> deletion calling folder), it creates the clip_pos_count_0 and other arrays with the length of 16569, which is the length of the human mtDNA genome.

However, this then only works for human application. I was writing to suggest adding the length as a user-specified parameter, or maybe finding cov and cov_out first, then use cov_out.shape to determine the length for clip_pos_count_0.

My solution for anyone with the same problem:

  1. Clone the github repository
  2. Change the length to match the mtDNA length of your species. This change is necessary in clifind.py file, lines 79-82 and line 120
  3. Build the package.

Best,
Christy

@caleblareau
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thanks for the note! we definitely had some tunnel vision when writing this. your edits make perfect sense to me and I will try to update the package in the coming weeks. Thank you !

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