[Bioc-devel] BamTallyParam argument 'which'

Michael Lawrence lawrence.michael at gene.com
Mon Feb 23 19:37:26 CET 2015

We just have to decide which is the more useful interpretation of which --
as a simple restriction, or as a vector of meaningful locii, which will be
analyzed individually? I would actually favor the first one (the same as
yours), just because it's simpler. To keep track of the query ranges, we
would need to add a new column to the returned object, which will more
often than not just be clutter. I guess we could introduce a new parameter,
"reduceWhich" which defaults to TRUE and reduces the which. If FALSE, it
instead adds the column mapping back to the original which ranges.

On Sun, Feb 22, 2015 at 2:36 PM, Thomas Sandmann <sandmann.thomas at gene.com>

> Hi Michael,
> ah, I see. I hadn't realized that returning the pileups separately for
> each region could be a desired feature, but that makes sense. I agree, as
> it is easy for the user to 'reduce' the ranges beforehand your first option
> (e.g. returning the ID of the range) would be more flexible.
> Perhaps you would consider adding a sentence to the documentation of
> 'which' on BamTallyParam's help page explaining that users might want to
> 'reduce' their ranges beforehand if they are only interested in a single
> tally for each base ?
> Thanks a lot !
> Thomas

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