On 05/01/2017 01:37, Martin Morgan wrote:
On 12/29/2016 12:25 PM, Vincent Carey wrote:A while ago Martin and I discussed the possibility of idempotence for TabixFile ... this seemed to make sense and soTabixFilefunction (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 programmingTabixFileListfunction (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.cast...@upf.edu>wrote:hi Lori,thanks for the clarification. if this is an intended change then i'd saythe 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)The original behavior has been restored; both TabixFile() and TabixFileList() are idempotent. Sorry for introducing the bug.Martin
great! thanks Martin!! robert.
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-boun...@r-project.org> on behalf of Robert Castelo <robert.cast...@upf.edu> *Sent:* Wednesday, December 28, 2016 11:50:58 AM *To:* bioc-devel@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-develThis email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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