Add IO helper for processing multiple alignments in a group #92
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gaoj66-roche wants to merge 4 commits into
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Add IO helper for processing multiple alignments in a group #92gaoj66-roche wants to merge 4 commits into
gaoj66-roche wants to merge 4 commits into
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Add grouped_unpaired_for_each_parallel and gaf_grouped_unpaired_for_each_parallel, which keep each read's alignments (a primary and its secondaries, grouped by read name) together in one call while still processing distinct groups in parallel. Batches are cut only at group boundaries: a batch keeps accepting reads until it holds at least batch_size reads and the next read starts a new group. This never splits a group across worker threads, at the cost of occasionally exceeding batch_size. Used by vg surject secondary promotion. Co-authored-by: Ona <no-reply@ona.com>
…econdary promotion was dropped vg surject's GAF+--promote-secondary path was removed because GAF carries no is_secondary flag and cannot distinguish primary from secondary alignments. gaf_grouped_unpaired_for_each_parallel was added solely to support that path so it is removed here. gaf_paired_interleaved_for_each is retained as it predates the secondary promotion work and is unrelated to it. Co-Authored-By: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>
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July 22, 2026 05:51
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This PR adds a helper
grouped_unpaired_for_each_parallelfor processing groups of alignments in parallel. This is introduced to support the secondary promotion feature (vgteam/vg#4973) where primary and secondary alignments need to be processed as a group.