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

Ryan C. Thompson rct at thompsonclan.org
Tue Dec 4 22:27:47 CET 2012

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?

-Ryan Thompson

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