torognes / vsearch

Versatile open-source tool for microbiome analysis
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--fastq_stats: remove option --output from the list of accepted options #572

Closed frederic-mahe closed 2 months ago

frederic-mahe commented 2 months ago

--fastq_stats accepts --option but does not do anything with it. If that option is not there for compatibility with usearch (which I need to check), then I suggest we remove it:

https://github.com/torognes/vsearch/blob/35d9e0031a9328390837d52a6537bc4609674a99/src/vsearch.cc#L3585

frederic-mahe commented 2 months ago

For usearch 5 to 11, test if command --fastq_stats accepts option --output and creates a corresponding file:

cd /tmp/

printf "@s\nA\n+\nI\n" > tmp.fastq

for USEARCH in usearch{5..11} ; do
    rm -rf tmp.output
    ${USEARCH} --fastq_stats tmp.fastq --output tmp.output
    ls -lh tmp.output
done

rm -rf tmp.output tmp.fastq

In summary:

usearch accepts --fastq_stats accepts --output creates output file
5 no no no
6 yes yes no
7 yes yes no
8 yes warning no
9 yes warning no
10 no no no
11 no no no

usearch 8 and 9 output a warning: WARNING: Option -output ignored. Option --output is clearly not intended to be used with command --fastq_stats. I decide to remove --output from the list of valid options for --fastq_stats (commit e4895e40608d17509ee470d600af3439f7204dad).