Fix WP genotype condition always evaluating to False in vcf_func.py - #261
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The condition checked if the string "WP" was a member of a list of lists
([x.split('=') for x in ...]), which can never be True. The fix extracts
only the key portion of each INFO field pair ([x.split('=')[0] for x in ...])
so the membership test works as intended for legacy NEAT WP genotype records.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…tests
Both WP code paths used 'for record in record[7].split(";")' which shadowed
the outer record list, causing a crash at the chrom/location assignments
that follow. Fixed by renaming the loop variable to info_item and, in the
has-format path, capturing record[9] before the loop begins.
Also adds tests/test_read_simulator/test_vcf_func.py with 14 tests covering:
- Path B (no FORMAT, WP in INFO): genotype matches WP value, slash/pipe
notation, WP among other fields, WP absent → random genotype
- Path A (FORMAT without GT, WP in INFO): genotype from WP
- Standard GT path: unaffected by WP fix
- General correctness: unknown chrom skipped, ref mismatch skipped,
missing QUAL defaulted
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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The condition checked if the string "WP" was a member of a list of lists ([x.split('=') for x in ...]), which can never be True. The fix extracts only the key portion of each INFO field pair ([x.split('=')[0] for x in ...]) so the membership test works as intended for legacy NEAT WP genotype records.