[BioC] a problem with trimLRPatterns

[wang peter]

i donot know why 0.1 mismatch can work to trim the correct adapter, but
if i set the max.Rmismatch from 1 to 9, it cannot work
thanks

> subject = "GGGAGTAAGAAAGGCACTGAAGGCACTATCAATAGATCGGAAGAGCGGTT"
> Rpattern = "CTGTAGGCACCATCAATAGATCGGAAGAGCGGTTCAGAAGGAATGCCGAG"

> trimLRPatterns(Rpattern = Rpattern, subject = subject, max.Rmismatch=1,with.Lindels=TRUE)
[1] "GGGAGTAAGAAAGGCACTGAAGGCACTATCAATAGATCGGAAGAGCGGTT"
> trimLRPatterns(Rpattern = Rpattern, subject = subject, max.Rmismatch=0.1,with.Lindels=TRUE)
[1] "GGGAGTAAGAAAGGCA"
> trimLRPatterns(Rpattern = Rpattern, subject = subject, max.Rmismatch=2,with.Lindels=TRUE)
[1] "GGGAGTAAGAAAGGCACTGAAGGCACTATCAATAGATCGGAAGAGCGGTT"
> trimLRPatterns(Rpattern = Rpattern, subject = subject, max.Rmismatch=3,with.Lindels=TRUE)
[1] "GGGAGTAAGAAAGGCACTGAAGGCACTATCAATAGATCGGAAGAGCGGTT"

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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