[Bioc-devel] BamTallyParam argument 'which'

Michael Lawrence lawrence.michael at gene.com
Mon Feb 23 19:52:10 CET 2015

We should at leaast try to avoid surprising the user. Seems like most
people expect "which" to be a simple restriction, so I think for now I will
just reduce the which, and if someone has a use case for separate queries,
we can address it in the future.

On Mon, Feb 23, 2015 at 10:41 AM, Thomas Sandmann <sandmann.thomas at gene.com>

> 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:
> https://stat.ethz.ch/pipermail/bioc-devel/2015-February/006978.html
> ---
> Thomas Sandmann, PhD
> Computational biologist
> Genentech, Inc.
> 1 DNA Way
> South San Francisco, CA 94080
> Phone: +1 650 225 6273
> Fax: +1 650 225 5389
> 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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