[Bioc-devel] Reading FASTQ/BAM from open file handle?
Ryan C. Thompson
rct at thompsonclan.org
Wed Dec 5 00:17:34 CET 2012
Perfect, that's just what I wanted for Fastq files. Is there no R
facility for reading unindexed bam?
On Tue 04 Dec 2012 02:47:56 PM PST, Martin Morgan wrote:
> 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
>> would be ideal, but in the short term, quip supports decompression to
>> 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)
> Rsamtools::scanBam is really expecting to read from an (indexed) bam
> file with random access.
>> -Ryan Thompson
>> Bioc-devel at r-project.org mailing list
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