Closed frederic-mahe closed 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).
--fastq_stats
accepts--option
but does not do anything with it. If that option is not there for compatibility withusearch
(which I need to check), then I suggest we remove it:https://github.com/torognes/vsearch/blob/35d9e0031a9328390837d52a6537bc4609674a99/src/vsearch.cc#L3585