Implement multi-threaded FastQ compression for umi-transfer #11
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alneberg
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… umi-transfer fails.
…afely the trait Send is not implemented for dyn ZWriter
…ing them to the output file.
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…the rexpect crate.
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umi-transfer 1.0.0 does its job, but the performance of the single-threaded tool is poor. I/O should be asynchronous to avoid blocking per-core threads, and this pull request implements such a functionality for the output files using the gzp crate. Inspiration how to incorporate it into the actual code was drawn from Crabz and Ouch, both MIT-licensed tools as well. Thread-pinning, albeit supported by
gzphas not been enabled because of the additional complexity involved.In a later PR, the input file logic will be slightly improved as well - not with multi-threading, but switching from flate2 decompression to gzp as well, to not use two libraries for the same purpose.
PS: 😟 Seems I have to fix the CI first...that Action uses no longer existing steps... which is being done in #12