[Bioc-devel] Reading FASTQ/BAM from open file handle?
Ryan C. Thompson
rct at thompsonclan.org
Tue Dec 4 22:27:47 CET 2012
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?
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