Input and Output Arguments

[lbergelson]

We've talked about adding @Input and @Output annotations.

My understanding of the mechanics of this is as such:
Rename @PositionalArguments to Input
A traversal will specify one Collection as the @Input for example, a ReadWalker will accept 1 or more Bams specified on the command line. How these are presented to the apply function is up to the traversal. In the case of read walkers they are likely to be merged and presented as a single ReadsDatasource.

on the command line this would look like

Hellbender CountReads bam1 bam2

Each tool implementing a traversal may specify 1 or more Outputs. These would be treated as standard arguments and it would be up to the tool or traversal to decide what to do with them.
ex

Hellbender PrintReads -O out.bam input.bam

Is this what we want?

[akiezun]

Yes, I think it is what we want. It would be consistent with the GNU standards. https://www.gnu.org/prep/standards/html_node/Command_002dLine-Interfaces.html
"It is usually a good idea for file names given as ordinary arguments to be input files only; any output files would be specified using options (preferably ‘-o’ or ‘--output’). Even if you allow an output file name as an ordinary argument for compatibility, try to provide an option as another way to specify it. This will lead to more consistency among GNU utilities, and fewer idiosyncrasies for users to remember."

By "ordinary arguments" they mean what you name "standard arguments".