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

[Ryan C. Thompson]

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
>> 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?
>
> ShortRead::FastqStreamer works with R connections, so for instance
> after example(FastqStreamer)
>
>   cmd = sprintf("cat %s", fl)
>   p = pipe(cmd)
>   strm = FastqStreamer(p, 50)
>   yield(strm)
>   yield(strm)
>
> Rsamtools::scanBam is really expecting to read from an (indexed) bam
> file with random access.
>
> Martin
>
>>
>> -Ryan Thompson
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>