Hi,
as fastq files are often compressed now, I would like to be able to write
out to compressed 'fq.gz' files, rather than raw text.

I have searched the BioC threads and found a similar topic at;

http://article.gmane.org/gmane.science.biology.informatics.conductor/45306/match=writeFastq

A poor example of what I would like to be able to achieve follows;

example(readFastq)
print(rfq)
fout <- "test.fq"
writeFastq(rfq, fout)
system(paste("gzip", fout))

but this does not compress the data as it is streaming out to file. I would
like to be able to do something like below, so this is a potential feature
request;

fout <- "test.fq.gz"
writeFastq(rfq, fout, compress=TRUE)

Is there an obvious way to compress using writeFastq that I am missing?


cheers,

Marcus


 sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  splines   stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] ShortRead_1.18.0     latticeExtra_0.6-24  RColorBrewer_1.0-5
 [4] Rsamtools_1.12.3     lattice_0.20-15      Biostrings_2.28.0
 [7] GenomicRanges_1.12.2 IRanges_1.18.0       BiocGenerics_0.6.0
[10] BiocInstaller_1.10.3 limma_3.16.7         Hmisc_3.12-2
[13] Formula_1.1-1        survival_2.37-4

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