Add VCF export support for SNP call datasets#1071
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adilraza99 wants to merge 5 commits intomalariagen:masterfrom
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Add VCF export support for SNP call datasets#1071adilraza99 wants to merge 5 commits intomalariagen:masterfrom
adilraza99 wants to merge 5 commits intomalariagen:masterfrom
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saadte
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| alleles = allele_chunk[j] | ||
| ref = str(alleles[0]) | ||
| alt_alleles = [str(a) for a in alleles[1:] if str(a) != ""] | ||
| alt = ",".join(alt_alleles) if alt_alleles else "." |
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How does this handle potential byte-backed nature of the values? Using str() in that case will lead to malformed vcf that cannot be used downstream.
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Thanks for pointing this out. This was something I had already been looking into while working on the exporter. I've updated the implementation to explicitly decode byte-backed allele values instead of relying on str(), and verified locally that REF/ALT are written correctly without any byte-string artifacts (e.g. b'A').
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Decode byte-backed allele values returned by snp_calls() (dtype |S1) before writing REF and ALT fields to the VCF. This prevents values like b'A' appearing in the output and ensures valid VCF formatting. All VCF exporter tests pass after this fix.
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Summary
Adds support for exporting SNP call datasets to Variant Call Format (VCF), enabling interoperability with common genomics tools and workflows.
Changes
VcfExportermixin following the existingPlinkConverterpatternsnp_calls_to_vcf()to export SNP calls directly to VCFAnophelesDataResourcetest_plink_converterpattern to verify output structure and dataset consistencyNotes
The implementation uses
snp_calls()as the data source so that multiallelic sites are preserved. VCF records are written incrementally from chunked genotype data to keep memory usage low when working with large datasets.closes #1054