Python3 related issue with cluster_reads.py found when running in targeted mode

[munrosa]

This is a bug report for your reference when you decide to update LinkedSV for compatibility with Python 3. This issue does not happen with Python 2.7, but does appear when using Python 3 and running LinkedSV in targeted mode.

GitHub/LinkedSV/scripts/cluster_reads.py", line 307, in calculate_num_reads_from_bcd21_file
line = line.strip().split(tab)
TypeError: a bytes-like object is required, not 'str'

[fangli80]

Hi,
Thank you for reporting this bug.
I tested on a WGS data set with Python 3.5.6 and didn't see this error. May I ask what exact python version do you use?

Best,
Li

[munrosa]

Sure, I used Python 3.7.5 in a conda install (Build h0371630_0).