[Bioc-devel] BamTallyParam argument 'which'
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. Leonard 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
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel