Add phase 2 streaming PLINK mount via vcztools.BedEncoder#3
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jeromekelleher wants to merge 3 commits intosgkit-dev:mainfrom
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Add phase 2 streaming PLINK mount via vcztools.BedEncoder#3jeromekelleher wants to merge 3 commits intosgkit-dev:mainfrom
jeromekelleher wants to merge 3 commits intosgkit-dev:mainfrom
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Serves .bed on demand from a per-FUSE-handle BedEncoder over a shared VczReader, with .bim/.fam precomputed once into in-memory bytes. Multiple processes opening the mount each get an independent encoder; iterators do not interfere across handles. Mount is refactored to accept a pyfuse3.Operations directly so phase-1 and phase-2 share the mount-loop machinery, and a new mount-plink-streaming CLI command is added. The fx_mounted_plink fixture is parametrised over passthrough/streaming so the plink1.9 / plink2 byte-identity assertions run in both modes.
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Serves .bed on demand from a per-FUSE-handle BedEncoder over a shared VczReader, with .bim/.fam precomputed once into in-memory bytes. Multiple processes opening the mount each get an independent encoder; iterators do not interfere across handles.
Mount is refactored to accept a pyfuse3.Operations directly so phase-1 and phase-2 share the mount-loop machinery, and a new mount-plink-streaming CLI command is added. The fx_mounted_plink fixture is parametrised over passthrough/streaming so the plink1.9 / plink2 byte-identity assertions run in both modes.