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Update to split sorted data sequentially and avoid simultaneous open files#2281

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whitwham merged 2 commits into
samtools:developfrom
vasudeva8:split1
Nov 28, 2025
Merged

Update to split sorted data sequentially and avoid simultaneous open files#2281
whitwham merged 2 commits into
samtools:developfrom
vasudeva8:split1

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@vasudeva8

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Fixes #2276
Updated sort to set sub-sort order when sorted with tags. This will set the SO as unsorted and SS as unsorted::.

On split, if the data is sorted by the tag with which it is being split, split is made sequentially instead of opening output files in parallel. If data is not sorted by the split key, split is made by opening output files in parallel as existed.

@whitwham whitwham merged commit 28c0f71 into samtools:develop Nov 28, 2025
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@vasudeva8 vasudeva8 deleted the split1 branch November 28, 2025 17:21
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Samtools split to open/close output files sequentially if file is ordered by split key

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