Proper command-line usage for fqgrep

[kockan]

The current README displays usage as:

fqgrep -r 'GACGAGATTA' -a 'GACGTGATTA' --r1-fastq /data/testR1.fastq.gz --r2-fastq /data/testR2.fastq.gz -o ./test_out -t 28

However, the way I'm currently testing the program looks like:

fqgrep --progress --threads 8 --color always <my_pattern> test.fastq test.fastq.gz test.fastq.zst

as the former command does not work and the latter seems to be in-line with the output of fqgrep -h , which is:

fqgrep [FLAGS] [OPTIONS] [--] [args]...

Which one of these is the long-term planned proper command-line usage? Happy to do a PR on the README if it should actually be changed, just wanted to confirm.

[nh13]

@kockan the intention is to have the command line options to match grep as much as possible, with no conflicts with bioinformatics-specific options (e.g. --reverse-complement). So the usage is very much out of date and the way you're testing it is the correct way. We'd welcome a PR!

And I am glad someone is using this other than ourselves!

[kockan]

#33

[msto]

@nh13 bumping this issue, I also noticed when opening #43 that the available CLI options don't match the usage described in the repo's README.