[Bioc-devel] Reading FASTQ/BAM from open file handle?

[Martin Morgan]

On 12/04/2012 01:27 PM, Ryan C. Thompson wrote:
> Hi all,
>
> I'm currently experimenting with using quip
> (https://github.com/dcjones/quip#readme) to save disk space when storing FASTQ
> and BAM files. One thing that would be nice is to read quip-compressed FASTQ or
> BAM files directly into R. Obviously direct support for reading quip compression
> would be ideal, but in the short term, quip supports decompression to standard
> output, so if I could have R read FASTQ or BAM data from an open file handle, I
> could pipe the decompressed output to R's FASTQ or BAM reader functions. Does
> anyone know if this is possible?

ShortRead::FastqStreamer works with R connections, so for instance after 
example(FastqStreamer)

   cmd = sprintf("cat %s", fl)
   p = pipe(cmd)
   strm = FastqStreamer(p, 50)
   yield(strm)
   yield(strm)

Rsamtools::scanBam is really expecting to read from an (indexed) bam file with 
random access.

Martin

>
> -Ryan Thompson
>
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