Note that rtracklayer has a function called FileForFormat that given a path will return a high-level file object, from either rtracklayer or Rsamtools, or anything that uses the naming convention [Format]File. rtracklayer could have coverage methods for the non-SAM/BAM files.
On Wed, Feb 12, 2014 at 6:15 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > On 02/12/2014 05:04 AM, Sean Davis wrote: > >> On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence < >> lawrence.mich...@gene.com >> >>> wrote: >>> >> >> This is a nice suggestion. What about integration with BiocParallel? >>> >>> >>> Yep, makes good sense. Since there is IO involved, one needs to be a >> bit >> careful about parallel ops, but I suspect that moderate parallel operation >> would be useful. >> > > I'd also suggest a method on character(), since a file (BAM or otherwise) > seems the most likely interpretation. Presumably this would chunk across a > single file and parallelize across multiple files, like summarizeOverlaps > (which uses bplapply). > > Martin > > > >> >> Michael >>> >>> >>> On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis <sdav...@mail.nih.gov> >>> wrote: >>> >>> It seems that the coverage method for BamFile() reads the entire BAM >>>> file >>>> into memory and then calls coverage. Is there a coverage method for >>>> BamFiles that does not read the entire BAM file into memory first? If >>>> >>> not, >>> >>>> does it make sense to augment the BamFile coverage method to do so in >>>> chunks? It is easy enough to write code to do so and there is even an >>>> example in the GenomicRanges HowTos, but having the method handle the >>>> use >>>> case would simplify matters just a bit. >>>> >>>> Thanks, >>>> Sean >>>> >>>> [[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-devel >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
