The FastqStreamer function works great for processing FASTQ files (e.g. adaptor/quality trimming) while keeping the memory footprint to a minimum. An equivalent convenience function for line-wise streaming through big BAM/SAM files would be a very useful addition too. Are there any plans for this? Thanks, Thomas

On 04/14/2012 01:43 PM, Thomas Girke wrote: > The FastqStreamer function works great for processing FASTQ files (e.g. > adaptor/quality trimming) while keeping the memory footprint to a > minimum. An equivalent convenience function for line-wise streaming > through big BAM/SAM files would be a very useful addition too. Are there > any plans for this? yes, maybe a slightly different interface; perhaps later this weekend. Martin > > Thanks, > > Thomas > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793