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multicore support for --info-file option #427

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SDmetagenomics opened this issue Nov 21, 2019 · 5 comments
Closed

multicore support for --info-file option #427

SDmetagenomics opened this issue Nov 21, 2019 · 5 comments

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@SDmetagenomics
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@SDmetagenomics SDmetagenomics commented Nov 21, 2019

is there still muticore support planned for the --info-file option, as I saw some further options were given support in issue #391 . Currently using cutadapt to trim adapters from paired end reads, and want to parse the different types of adapters present in large paried end fastq files, which takes a long time with one core using the --info-file option. Also, totally fine it just provides info about forward read (R1) only, but would be great if It could use more cores for speedup.

  • Cutadapt v2.5 on Python 3.6.5
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@marcelm marcelm commented Nov 21, 2019

This is planned, but until now, no one has asked for it so I haven’t prioritized it. Since you do ask now, I can look into this for one of the next versions.

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@SDmetagenomics SDmetagenomics commented Nov 21, 2019

@marcelm marcelm closed this in df3cf9e Nov 22, 2019
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@marcelm marcelm commented Nov 22, 2019

This is now implemented. I think I’ll make a new release now, so Cutadapt 2.7 should support this. If you have time, can you please test creating an info file with and without multicore and check whether the two output files are identical? I have some automated tests, but I don’t know whether they cover all the corner cases.

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@SDmetagenomics SDmetagenomics commented Dec 5, 2019

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@marcelm marcelm commented Dec 5, 2019

Great, thanks for the feedback! :-)

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