[Bioc-sig-seq] how to sort reads by ids

[Martin Morgan]

On 09/18/2011 10:10 AM, wang peter wrote:
> thx
> i know how to sort reads by ids
>
>
> rm(list=ls())#
> fastqfile="query.fastq"
> library(ShortRead)
> reads<- readFastq(fastqfile);#
> ids<- as.character(id(reads)); #
> ids<- sort(ids, method = "sh", index.return=TRUE)

   idx = order(id(reads))
   reads[idx]

Advanced: sort / order / rank are tricky on character() vectors; they 
obey LOCALE collation order Sys.getlocale(). Use Sys.setlocale(locale="C")

Martin


> reads<-reads[ids$ix]
>
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