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fa2fq help text is the same as fq2fa #45

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scwatts opened this issue Sep 6, 2018 · 0 comments
Open

fa2fq help text is the same as fq2fa #45

scwatts opened this issue Sep 6, 2018 · 0 comments

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@scwatts
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scwatts commented Sep 6, 2018

Thank you for creating and publishing this tool. It has been very useful to many people and I'd like to contribute in a small way to your project. I noticed that the help text and arguments for fa2fq is not correct and appears to be copied from fq2fa without any changes:

./bin/fa2fq 
not enough parameters
fq2fa - Convert Fastq sequences to Fasta sequences.
Usage: fq2fa tmp.fq tmp.fa [...] 
       fq2fa --paired tmp.fq tmp.fa
       fq2fa --merge tmp_1.fq tmp_2.fq tmp.fa
Allowed Options: 
      --paired                           if the reads are paired-end in one file
      --merge                            if the reads are paired-end in two files
      --filter                           filter out reads containing 'N'

This is confusing as fa2fq only accepts two positional arguments (a fasta input filepath and a fastq output filepath). None of the options in the help text are used and if you follow the usage help you'll end up with unexpected results.

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