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…nt index before reading dosages, so only the requested variants are loaded
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keepVariantsPathandkeepIndelwere applied after the dosage matrix for the whole region was read, so asking for a few variants still loaded every genotype in the region (300 chr22 variants over the full chromosome tried to allocate 14.8 GB). The filters are now applied to the variant index before the read, so only the kept variants are loaded. Output is unchanged; a new test checks that the kept dosages equal a full load followed by subsetting.