Hi Martin,
Thanks for your reply.
I've take a look at the file and you are right the problem arise of an
abnormal termination of the conversion from scarf to fastq on that file.
problem corrected and things are running smooth now.
Have a nice day.
Regards,
Ramzi
----------------------------------------------------------------


On Wed, Jan 6, 2010 at 9:30 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi --
>
> Ramzi TEMANNI wrote:
> > Hi,
> > I'm using the following function to extract a subselection of reads based
> on
> > their ID from a FastQ file:
> > extract.reads.fq<-function(dir,fq.file,id.list)
> > {
> > rfq <- readFastq(dir, pattern=fq.file)
> > tmp=extract.id(rfq)
> > sv.reads=rfq[which(id.list%in%tmp)]
> > writeFastq(sv.reads, paste("sv_",fq.file,sep=""))
> > }
> >
> > The function works well but for one file i got the following error :
> > Error in .local(dirPath, pattern, ...) :
> >   ShortRead internal: too many 'snap' entries
>
> Probably the format of the one file is causing problems -- maybe a
> missing new line after the last file record?
>
> Can you post the result of sessionInfo(), and if the format of the file
> is not obviously wrong can you make it available to me?
>
> Martin
>
>
> > Tried to google it but nothing is coming out, anyone encoutred this error
> ?
> >
> > Thanks in advance for your help.
> >
> >
> >
> >
> > ----------------------------------------------------------------
> > Kind regards / Met vriendelijke groet,
> > Mohamed-Ramzi Temanni,
> > ----------------------------------------------------------------
> >
> >       [[alternative HTML version deleted]]
> >
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> > Bioc-sig-sequencing@r-project.org
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>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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