[BioC] is matchPattern faster?

[Harris A. Jaffee]

Sorry, I'll get it eventually.

	answer = which.isMatchingAt("N", seqs, at=6:1, follow.index=TRUE)

Let me know if anything beats it.

On Jan 19, 2012, at 6:15 PM, Harris A. Jaffee wrote:
> 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)
>>>
>>>
>>>
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