[BioC] readFastq, writeFastq, compressed files and unix pipes.

[Ivan Gregoretti]

Hello ShortRead developers,

I recently tried to create an R script that could run as an ordinary
programme at the command line. It was something like

$ R --vanilla --slave -f ./myscript.R --input=input.fastq.gz
--output=output.fastq.gz

I tried and failed but I learned something in the process: readFastq()
and writeFastq() are not symmetrical.

Specifically:

1) readFastq() can tell the difference between a plain text FASTQ file
and a gzipped FASTQ file (.gz). Unlike that, writeFastq() always
outputs in plain text regardless of the suffix passed.

2) writeFastq() understands unix pipes because it conveniently accepts
the file argument "/dev/stdout". Unlike that, readFastq() does not
accept the file argument "/dev/stdin", so, no pipes are possible.

It would be great if readFastq() and writeFastq() were equally smart.
Please consider adding these functionalities.

Thank you,

Ivan





Ivan Gregoretti, PhD