Allow using multiple threads to (de)compress hts files #74
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This would be great! One suggestion, I would set the default number of (de)compression threads to be the max of 1 and 25% of the total requested threads. This isn't a perfect heuristic, but after playing with samtools on a lot of different systems and use cases, I find myself almost always doing this. |
milkschen
changed the title
This reverts commit 005544f.
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@mrvollger many thanks for the suggestion! I updated the PR to apply the logic. |
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Link to the issue: #72 |
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Updates the
--threads (-t)logic to allow using multiple threads to (de)compress HTS files. This can improve thread scaling.The threads are split into two pools: lift (
--lift_threads) and hts (--hts_threads). Users can specify them explicitly, or leverage the auto thread inference algorithm: withtthreads assigned to leviosam2,max(1, t/4)threads are assigned to HTS and the rest are assigned to the lift core.