[BioC] is matchPattern faster?

[Harris A. Jaffee]

Perhaps something along the lines

	r = reverse(narrow(seqs, 1, 6))
	answer = 7 - which.isMatchingAt("N", r, at=1:6)

On Jan 19, 2012, at 5:26 PM, wang peter wrote:
> i have some reads from illumina sequencer
> there are some "N" in the reads
> i want to find the last "N" in the first 6 bp of the sequence
> so do you think matchPattern is faster ? or other low-level match methods?
> 
> 	reads <- readFastq(fastqfile)
> 	seqs <- sread(reads);
>                  matchPattern("N", seqs)
> 
> 
> 
> -- 
> shan gao
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