Feature Request: Report the Space type

[tomck]

As getSpaceType() is an option in libStatGen it would be nice to be able to use fastQValidator to both validate the fastq and report the space (color or base), for use in scripts.

[mktrost]

I just made an update in a new branch, spaceType. Is this what you had in mind? If so, I will push it to master. If not, let me know, and I can change it. Sorry for the delayed response to your request.

[tomck]

Looks like it mostly, although I was kind of hoping for a flag so it could be used in 'if' sections of scripts as in this code: if ( $(fastqvalidator --spacetype $1) == "base" );

[mktrost]

So for the --spacetype flag, would you want it to just report spacetype (color/base/unknown) to stdout and write nothing else to stdout (the effect of running --quiet with the exception of the space type output)?
When that flag is specified, should it also validate, or would you make two calls? If it validates, then that result would only be reflected via the return value - any error messages would be suppressed so only the spaceType is written to stdout.

[tomck]

Interesting preposition, results could be base, color, unknown, or invalid (I assume if it's unknown it's probably invalid so that might be redundant?)