name 'overlap' is not defined in extract_barcodes.py

[jinfengzou-uhn]

Describe the bug

name 'overlap' in line 79 is not defined in extract_barcodes.py and a DeprecationWarning for 'U' mode in line 156 and 157

To Reproduce

Steps to reproduce the behavior:

1. Go to 'ConsensusCruncher/extract_barcodes.py'
2. Use commands 'ConsensusCruncher/extract_barcodes.py --read1 --read2 --outfile --blist'
3. Use inputs available at '...'
4. See error

Expected behavior

Extract UMI barcode

Screenshots

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System (please complete the following information):

• OS: Linux
• Software versions: Feb 14, 2020

Additional context

Add any other context about the problem here.

Relevant inputs

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[mawusseAgbessi]

Hi,
I'm having the same issue! Did you find a solution to this issue?
Many thanks in advance

[jinfengzou-uhn]

Hi,
I'm having the same issue! Did you find a solution to this issue?
Many thanks in advance

Hi mawusseAgbessi,

"Overlap" issue has been corrected by removing "line 79". It's been updated.
If you have the same issue of "DeprecationWarning for 'U' mode in line 156 and 157", then change 'rU' to 'r'. It could be caused by python version. This tools is developed on python 3.5.1. I used python 3.7.2.

[mawusseAgbessi]

Hi jinfengzou-uhn ,
Thanks you so much for the quick reply; It helps a lot. I am using python 3.7.0. It is working now.