[Bioc-devel] TabixFileList() constructor broken in devel

[Vincent Carey]

A while ago Martin and I discussed the possibility of idempotence for
TabixFile ... this seemed
to make sense and so

> TabixFile

function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize =
NA_integer_)

{

    if (is(file, "TabixFile"))

        return(file)

    tryCatch({

        .io_check_exists(c(file, index))

    }, error = function(err) {

        stop(sprintf("TabixFile: %s", conditionMessage(err)),

            call. = FALSE)

    })

    .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize,

        ...)

}

<environment: namespace:Rsamtools>


TabixFileList could behave similarly, working either from character paths,
or from

a list of TabixFile instances, or from a TabixFileList ... might be a
design practice to

promote for S4 programming


> TabixFileList

function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize =
NA_integer_)

{

    index <- as.character(index)

    .RsamtoolsFileList(file, index, ..., yieldSize = yieldSize,

        class = "TabixFile")

}

<environment: namespace:Rsamtools>

On Thu, Dec 29, 2016 at 11:55 AM, Robert Castelo <robert.castelo at upf.edu>
wrote:

> hi Lori,
>
> thanks for the clarification. if this is an intended change then i'd say
> the documentation needs to be updated since, as i showed in my email
> below, it currently says that for functions such as 'TabixFileList()'
> the input 'file' argument should be a 'TabixFile' instance and not a
> character vector.
>
> this change also means the input is switching from a 'TabixFile'
> instance to a 'character' vector, so pipelines or packages doing calls
> to 'TabixFileList()' that have been passing 'TabixFile' instances as
> arguments will have to update those calls to pass a character vector.
>
>   i'd suggest that if there's no good reason to switch, it would be
> safer to add the character vector as an additional possibility in the
> input argument 'file', just as with 'countTabix()', and minimize
> possible breaks of pipelines/packages using 'TabixFileList()'. i've
> encountered this problem because my own package VariantFiltering calls
> 'TabixFileList()' although is not a big deal to fix it.
>
> cheers,
>
> robert.
>
> On 28/12/2016 19:44, Shepherd, Lori wrote:
> >
> > Thank you for bringing this to our attention. There were some updates
> > made a few weeks ago to the behavior and input of 'TabixFileList()' .
> >  Its current implementation will work with a character vector as
> > input.  I will investigate further into why this change was made and
> > if it needs to be addressed.
> >
> >
> > In the meantime:
> >
> > TabixFileList(tbx)
> > will throw an ERROR, but you can still use the same file that was used
> > to create the TabixFile
> > tbx <- open(TabixFile(fl, yieldSize=100))
> > TabixFileList(fl)
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ------------------------------------------------------------------------
> > *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
> > Robert Castelo <robert.castelo at upf.edu>
> > *Sent:* Wednesday, December 28, 2016 11:50:58 AM
> > *To:* bioc-devel at r-project.org
> > *Subject:* [Bioc-devel] TabixFileList() constructor broken in devel
> > hi,
> >
> > the 'TabixFileList()' constructor in Rsamtools seems to be broken in
> > devel:
> >
> > library(Rsamtools)
> > example(TabixFileList) ## which actually does not construct any
> > 'TabixFileList'
> > TabixFileList(tbx)
> > Error in as.vector(x, "character") :
> >    cannot coerce type 'environment' to vector of type 'character'
> >
> > while in release this works fine:
> >
> > library(Rsamtools)
> > example(TabixFileList) ## which actually does not construct any
> > 'TabixFileList'
> > TabixFileList(tbx)
> > TabixFileList of length 1
> > names(1): example.gtf.gz
> >
> > the man page has not changed between devel and release and the current
> > description of the argument 'file' supports the use of a 'TabixFile'
> > instance as input:
> >
> >      file: For TabixFile(), A character(1) vector to the tabix file
> >            path; can be remote (http://, ftp://). For ‘countTabix’, a
> >            character(1) or ‘TabixFile’ instance. For others, a
> >            ‘TabixFile’ instance.
> >
> > please find below my session information for the devel run.
> >
> > thanks!
> >
> > robert.
> >
> > sessionInfo()
> > R Under development (unstable) (2016-11-17 r71661)
> > Platform: x86_64-apple-darwin16.1.0 (64-bit)
> > Running under: macOS Sierra 10.12.2
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> > [8] methods   base
> >
> > other attached packages:
> >   [1] Rsamtools_1.27.9      Biostrings_2.43.1 XVector_0.15.0
> >   [4] GenomicRanges_1.27.17 GenomeInfoDb_1.11.6 IRanges_2.9.14
> >   [7] S4Vectors_0.13.5      BiocGenerics_0.21.1 setwidth_1.0-4
> > [10] colorout_1.1-0
> >
> > loaded via a namespace (and not attached):
> > [1] zlibbioc_1.21.0    compiler_3.4.0 tools_3.4.0 BiocParallel_1.9.3
> > [5] bitops_1.0-6
> >
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