Hello
 In the example below, Rpattern2 (2 mismatches) trims the subject correctly, while Rpattern3 (3 mismatches) which is not supposed to do any trimming, it trims the last 2 nucleotides. Can you explain why?


> subject <- DNAStringSet("GCTGGAACCCAGGGTGTTGTACCTGTAGGCACCA")
> Rpattern2 <- "CTGaAGGCACgA" # 2 mismatches
> Rpattern3 <- "tTGaAGGCACgA" # 3 mismatches
> trimLRPatterns(Rpattern = Rpattern2, subject = subject, max.Rmismatch = rep(2, 12))
  A DNAStringSet instance of length 1
    width seq
[1]    22 GCTGGAACCCAGGGTGTTGTAC
> trimLRPatterns(Rpattern = Rpattern3, subject = subject, max.Rmismatch = rep(2, 12))
  A DNAStringSet instance of length 1
    width seq
[1]    32 GCTGGAACCCAGGGTGTTGTACCTGTAGGCAC


> sessionInfo()
R version 2.10.0 alpha (2009-10-01 r49909) 
x86_64-apple-darwin9.8.0 

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rtracklayer_1.5.17 RCurl_1.2-0        bitops_1.0-4.1     ShortRead_1.3.36  
[5] lattice_0.17-25    BSgenome_1.13.16   Biostrings_2.13.48 IRanges_1.3.87    

loaded via a namespace (and not attached):
[1] Biobase_2.5.8 grid_2.10.0   hwriter_1.1   tools_2.10.0  XML_2.6-0    
> 


      
	[[alternative HTML version deleted]]

