Hi, > More generally I'd like to implement something to process larger files. > The conversations I've had have involved 'streams' where the file > essentially gets processed in chunks. The user would have to provide a > function that processed the appropriate data structure, e.g., an > 'AlignedRead' or 'ShortReadQ' object, and possibly also a function that > stitched the results from several chunks back together.
I think one could get a lot of mileage out of this. For instance, I think for QA type of stuff, being able to rip through a fastq file and process 1 fastq "object" (the 4 (or so) lines you get per read) would be very handy. -- 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
