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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