[BioC] [Bioc-sig-seq] ShortRead internal: too many 'snap' entries

[Martin Morgan]

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,
> ----------------------------------------------------------------
> 
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> 
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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