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ngless-toolkit / ngless

NGLess: NGS with less work
https://ngless.embl.de
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ngless copies files untouched if they are written after reading #59

Closed unode closed 6 years ago

unode commented 6 years ago 
sample/A.pair.1.fq.gz
sample/A.pair.2.fq.gz
sample/B.pair.1.fq.gz
sample/B.pair.2.fq.gz
sample/C.single.fq.gz
ngless "0.0"
import "mocat" version "0.0"

input = load_mocat_sample('sample')
write(input, ofile='tmpdir/output.fq')

Produces output.pair.1.fq, output.pair.2.fq, output.single.fq all in the original compression instead of following the extension provided. If the same files are re-read afterwards ngless will fail to parse since it relies on the file extension (not the MIMEtype) to recognize the format.