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Fix WP genotype condition always evaluating to False in vcf_func.py #261

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Merged
joshfactorial merged 2 commits into from
Apr 7, 2026
Merged

Fix WP genotype condition always evaluating to False in vcf_func.py #261

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9456184
Fix WP genotype condition always evaluating to False in vcf_func.py
joshfactorial Apr 5, 2026
f5411de
Fix variable shadowing in WP genotype parsing blocks; add regression …
joshfactorial Apr 6, 2026
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20 changes: 10 additions & 10 deletions neat/read_simulator/utils/vcf_func.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,19 +161,20 @@ def parse_input_vcf(
# Retrieve the GT from the first sample in the record
genotype = retrieve_genotype(record)

elif "WP" in [x.split('=') for x in record[7].split(';')]:
elif "WP" in [x.split('=')[0] for x in record[7].split(';')]:
"""
"WP" is the legacy code NEAT used for genotype it added. It was found in the INFO field.
We're just going to make a sample column in this version of NEAT
The logic of the statement is split the info field on ';' which is used as a divider in that field.
Most but not all fields also have an '=', so split there too, then look for "WP"
"""
format_column = f"GT:{record[8]}"
for record in record[7].split(';'):
if record.startswith('WP'):
genotype = record.split('=')[1].replace('/', '|').split('|')
sample_field = record[9]
for info_item in record[7].split(';'):
if info_item.startswith('WP'):
genotype = info_item.split('=')[1].replace('/', '|').split('|')
genotype = np.array([int(x) for x in genotype])
normal_sample_field = f"{get_genotype_string(genotype)}:{record[9]}"
normal_sample_field = f"{get_genotype_string(genotype)}:{sample_field}"

else:
format_column = 'GT:' + record[8]
Expand All @@ -182,18 +183,17 @@ def parse_input_vcf(
gt_field = get_genotype_string(genotype)
normal_sample_field = f'{gt_field}:{record[9]}'

elif "WP" in [x.split('=') for x in record[7].split(';')]:
elif "WP" in [x.split('=')[0] for x in record[7].split(';')]:
"""
"WP" is the legacy code NEAT used for genotype it added. It was found in the INFO field.
We're just going to make a sample column in this version of NEAT
The logic of the statement is split the info field on ';' which is used as a divider in that field.
Most but not all fields also have an '=', so split there too, then look for "WP"
"""
format_column = "GT"
info_split = record[7].split(';')
for record in info_split:
if record.startswith('WP'):
genotype = record.split('=')[1].replace('/', '|').split('|')
for info_item in record[7].split(';'):
if info_item.startswith('WP'):
genotype = info_item.split('=')[1].replace('/', '|').split('|')
genotype = np.array([int(x) for x in genotype])
normal_sample_field = get_genotype_string(genotype)

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