Steve Lianoglou wrote: > Hi, > > Not a pressing issue, but I feel like I'm doing this wrong. > > Currently in order to get all the reads on a chromosome using > Rsamtools (to extract from a BAM file), I'm making an IRanges object > that's "as long" as the chromosome I want the reads for. > > For instance, for chr1: > > which <- RangesList(chr1=IRanges(start=1, end=247249719)) > params <- ScanBamParams(which=which) > reads <- scanBam(my.bam.file, param=params)[[1]] > > Is there are "better" way to do it, eg. w/o making the IRanges object > that's stretches over the chromosome?
I don't think so, though 'end' doesn't have to be a literal end, e.g,. .Machine$integer.max and 'stretches' doesn't really involve any cost -- just two numbers. The use case I was thinking of was a well-defined collection of regions of interest, probably coming from some genome annotation, but I guess you're interested in chromosome-at-a-time processing? Martin > > Just curious, thanks. > -steve > -- Martin Morgan 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
