feat(io): bound coordinate-sort memory with an external merge - #214
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alejandrogzi wants to merge 2 commits into
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feat(io): bound coordinate-sort memory with an external merge#214alejandrogzi wants to merge 2 commits into
alejandrogzi wants to merge 2 commits into
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'--outSAMtype BAM SortedByCoordinate' no longer buffers the whole output in RAM. The sort now fills a '--limitBAMsortRAM' buffer, spills sorted runs beside the output, and k-way merges them on finish, so peak memory is flat in output size. '--limitBAMsortRAM 0' now means 512 MiB instead of unlimited, and runs beyond 64 are merged in balanced passes so a small budget cannot exhaust file descriptors. Output is byte-identical to the previous in-memory sort.
A low --limitBAMsortRAM must spill sorted runs to disk and merge them into a BAM identical to the unbounded in-memory sort, leave no scratch behind, and emit non-decreasing (chrom, pos) order.
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--outSAMtype BAM SortedByCoordinatespill to disk instead of buffering the whole output in RAM.--limitBAMsortRAMbuffer, spills sorted runs beside the output, and k-way merges them on finish; peak memory is flat in output size.--limitBAMsortRAM 0now means 512 MiB instead of unlimited; values above 0 spill above the limit rather than aborting.EMFILE).Behavior change vs. before: the default bounded budget replaces the previous unlimited buffering.
Tests:
cargo test --releasegreen.