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dcjones / quip

Compressing next-generation sequencing data with extreme prejudice.
http://www.cs.washington.edu/homes/dcjones/quip/
BSD 3-Clause "New" or "Revised" License
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Handle compressed fastq files as input #13

Closed DarwinAwardWinner closed 11 years ago

DarwinAwardWinner commented 11 years ago

Sometimes fastq files are delivered gzipped. Currently one has to do something like the following in order to compress such files with quip: zcat input.fastq.gz | quip -i fastq -a -c > output.fastq.qp. It would be nice if quip natively supported compressed input for fastq files.

dcjones commented 11 years ago

That's not a bad idea, and not hard to do. I'll keep this issue open and try to get to it in the next couple weeks.

dcjones commented 11 years ago

I've implemented support for directly reading fastq files compressed with gzip and bzip2. You can use it by building from the git repository, but I'll release a new version/tarball in the next few days with it included.