Documentation improvement suggestion

[hazmup]

Hi and thank you for the great tool!

I believe that the documentation on the behavior of the --unmapped-reads --unpaired-reads --chimeric-pairs parameters (and maybe their naming), is lacking and thus misleading. Depending on the downstream application (as in my case I need proper fastq files), it may not be the desired or expected behavior at all. As it is now it takes a considerable amount of time and effort to understand that when the use value is selected, only one of the reads in a pair will be kept. And even then it is not immediately obvious which one. Expanding on this would be helpful to a lot of users, considering there are several issues opened on the matter.

Let me know what you think.
Best,
Stelios

[TomSmithCGAT]

Hi @hazmup - Always happy to consider updating documentation for clarity. Would you be able to make suggestions in a pull request, or failing that, give some suggested text here?

[IanSudbery]

Hi @TomSmithCGAT I started making some documentation changes on {IS}-Documentation-for-orphan-reads