[BioC] Is there any way to merge all yeilds of FastqStreamer?

[Martin Morgan]

On 01/24/2012 05:12 AM, Prashantha Hebbar wrote:
> Hello friends,
>
> I wanted to know a way to merge all yeilds of FastqStreamer as one ShortReadQ object. Can anybody suggestme a way to do this?
>
> readFq<- lapply(paste(inDataPath,fqFiles,sep=""),
>                          function(fqFiles){
>                                  fQ<-FastqStreamer(fqFiles,n=1e6)
>                                  while(length(readsFq<- yield(fQ))){
>                                         # Collect all chunks
>                                  }
>                              return(AllinOneShortReadQ)
>
>                          })

FastqStreamer returns ShortReadQ objects, these can be appended with 
append(), but if the objective is to read in a fastq file then use 
readFastq.

Martin

> Regards,
> Prashantha
> 	[[alternative HTML version deleted]]
>
>
>
>
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