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Convert string None to Python None #218

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tyamaguchi-ucla
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@tyamaguchi-ucla tyamaguchi-ucla commented May 2, 2024

Description

As described in #208, it appears that the conversion of the string "None" to the python None object wasn't implemented in the parse_combine_counts_args function unlike the ‎parse_combine_counts_fw_args‎ function. This results in the error shown in #208. Therefore, it seems that the phase_snps step is not treated as optional when fixed_width = False.

Closes #208

Testing Results

When

[combine_counts]
# Path to phased file; leave as "None" to run hatchet without phasing
phase = "None"

It successfully passed check without failing.

NO PHASING FILE FOUND at /path/phased.vcf.gz. Not including phasing in binning process.
[2024-May-01 21:28:51]# Parsing and checking input arguments

@mmyers1 @balabanmetin Please let me know if you want me to run additional tests.

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simple change, looks fine

@mmyers1 mmyers1 merged commit 7830580 into raphael-group:master May 2, 2024
2 of 4 checks passed
@tyamaguchi-ucla tyamaguchi-ucla deleted the tyamaguchi-ucla-convertStringNone branch May 2, 2024 19:00
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String "None" is not converted to Python None object in parse_combine_counts_args
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