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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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Auto format to select compression choice for output #13

Closed khyox closed 7 years ago

khyox commented 7 years ago

Hello Ryan,

First of all, thank you very much for Porechop, it is fabulous! I am using it with custom barcoding in adapters.py and my first testings are promising.

This is more a feature request, but I would expect to have an uncompressed output if the input is uncompressed, specially with the auto choice for the format flag. Another option is to extend the choices to something like {auto,fasta,fastq,fastagz,fastqgz} and avoid forced gzipping the output. Whatever... this is just a suggestion and a good excuse to thank you for Porechop.

rrwick commented 7 years ago

That's a good idea, and since I've been working on Porechop recently, I decided to quickly implement this while the code's still fresh in my head.

I think it's all working now on the master branch. The format option are pretty much as you suggested, but I put a dot in the gzipped ones: {auto,fasta,fastq,fasta.gz,fastq.gz}

Give it a try and let me know if anything's not right!

khyox commented 7 years ago

Tried and all running smoothly! Thank you very much Ryan!