feat: Add VCF export support for SNP call datasets (GH-1054)#1197
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khushthecoder wants to merge 7 commits intomalariagen:masterfrom
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feat: Add VCF export support for SNP call datasets (GH-1054)#1197khushthecoder wants to merge 7 commits intomalariagen:masterfrom
khushthecoder wants to merge 7 commits intomalariagen:masterfrom
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Adds a VcfConverter mixin following the existing PlinkConverter pattern: - New VcfConverter class in malariagen_data/anoph/to_vcf.py with snp_calls_to_vcf() method for exporting SNP calls to VCF format - Streams data in chunks to keep memory usage low on large datasets - Explicitly decodes byte-backed allele values to prevent artifacts - Uses snp_calls() as data source to preserve multiallelic sites - Integrated into AnophelesDataResource via MRO - Tests follow the test_plink_converter pattern Closes malariagen#1054
variant_contig stores integer indices (dtype u1), not string names. The check 'contig_chunk.dtype.kind == "S"' was never true, so CHROM values were written as '0', '1', '2' instead of actual contig names like '2R', '2L', '3R'. Fix: Use ds.attrs['contigs'] to map integer indices to contig names, following the established pattern in snp_frq.py and aim_data.py. Also: - Add ##contig header lines for VCF spec compliance - Update test to verify CHROM values match actual contig names
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@jonbrenas — All checks, including the recent pre-commit / ruff-format linting steps, are now passing perfectly. The codebase correctly handles byte- decoding without native dependencies and handles chunk-streaming with minimal memory overhead, thoroughly validated by the new tests. Could you please take a look when you have a moment? Let me know if you need any final tweaks. |
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Fix: #1054 — SNP calls to VCF export
Summary
Adds support for exporting SNP call datasets to Variant Call Format (VCF), enabling interoperability with common genomics tools and workflows such as
bcftools,GATK, and R pipelines.Changes
VcfConvertermixin following the existingPlinkConverterpatternsnp_calls_to_vcf()to export SNP calls directly to.vcfformatb'A'-style artifacts in the outputsnp_calls()as the data source so that multiallelic sites are preserved (standard for VCF)AnophelesDataResourcevia the existing cooperative MROvcf_params.pyfollowing theplink_params.pypattern for type-annotated parameterstest_plink_converterpattern to verify output structure, header correctness, sample ID matching, variant positions, and overwrite behaviorFiles Changed
malariagen_data/anoph/to_vcf.pyVcfConvertermixin withsnp_calls_to_vcf()malariagen_data/anoph/vcf_params.pymalariagen_data/anopheles.pyVcfConvertertests/anoph/test_vcf_converter.pyNotes
overwriteparameter controls whether existing output files are regenerated or reused