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Handling missing QUAL in user VCF files #163

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Merged
joshfactorial merged 1 commit into from
Oct 2, 2025
Merged

Handling missing QUAL in user VCF files #163

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5 changes: 5 additions & 0 deletions neat/read_simulator/utils/vcf_func.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,11 @@ def parse_input_vcf(input_dict: dict[str: ContigVariants],
f'{reference_string}')
continue

# Quality score could be missing, in this case, we treat it as ground truth and assign a default score
default_qual = "42"
if record[5] == ".":
record[5] = default_qual

# We'll need the genotype when we generate reads, and output the records, if applicable
genotype = None
normal_sample_field = None
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