[Bioc-devel] BamTallyParam argument 'which'

Leonard Goldstein goldstein.leonard at gene.com
Mon Feb 23 20:05:28 CET 2015

Hi Michael and Thomas,

I ran into the same problem in the past (i.e. when I started working
with functions like scanBam I expected them not to return the same
alignment multiple times)

One thing to consider might be that returning alignments multiple
times is consistent with the behavior of the samtools view command.
Quoting from the samtools manual:

“Important note: when multiple regions are given, some alignments may
be output multiple times if they overlap more than one of the
specified regions.”

Maybe there is an argument for keeping things consistent with
samtools? As you said, if documented properly, the user can decide
whether to reduce regions specified in which or not.


On Mon, Feb 23, 2015 at 10:52 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> 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>
> wrote:
>> 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
>> USA
>> 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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