[Bioc-devel] BamTallyParam argument 'which'

Thomas Sandmann sandmann.thomas at gene.com
Mon Feb 23 19:41:14 CET 2015

Personally, I don't have a use case with "meaningful loci" worth tracking,
so keeping it simple would work for me.

Incidentally, would it be good to deal with the 'which' parameter in a
consistent way across different methods ? I just saw this recent post on
the mailing list in which a used got confused by duplicate counts returned
after passing 'which' to scanBamParam:



Thomas Sandmann, PhD
Computational biologist

Genentech, Inc.
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Email: sandmann.thomas at gene.com

"If a man will begin with certainties, he shall end in doubts; but if he
will be content to begin with doubts he shall end in certainties." -- Sir
Francis Bacon

On Mon, Feb 23, 2015 at 10:37 AM, Michael Lawrence <
lawrence.michael at gene.com> wrote:

> 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
> > wrote:
>> 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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