Hi Martin, On Thu, Jan 7, 2010 at 1:11 AM, Martin Morgan <[email protected]> wrote: <snip>
>> 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. Yeah, I know re: no real cost -- was just curious is all. Good point on simply using $integer.max, though. > 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? Yup -- I've been creating some libraries to help deal with *-seq experiments + data and didn't really have a good way to store and load the reads quickly until I tried BAM files. Although Rsamtools + BAM files are really fast, I still like to pull all of my reads per chromosome into an IntervalTree and do whatever batch processing I need to against that. Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
