[BioC] is matchPattern faster?

[Harris A. Jaffee]

Or maybe

	n = narrow(seqs, 1, 6)
	answer = 6 - nchar(sub(".*N", "", n))

On Jan 19, 2012, at 6:01 PM, Harris A. Jaffee wrote:
> 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
>> Room 231(Dr.Fei lab)
>> Boyce Thompson Institute
>> Cornell University
>> Tower Road, Ithaca, NY 14853-1801
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>> 
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