dear harris: thank you very much for your previous help, but i am still confused by such problems: [1] why does the second section of coding can not work,but the first can subject = "TTTACGT" Lpattern = "TTTAACGT" trimLRPatterns(Lpattern = Lpattern, subject = subject, max.Lmismatch=1,with.Lindels=TRUE) subject = "TGCATTT" Rpattern = "TGCAATTT" trimLRPatterns(Rpattern = Rpattern, subject = subject, max.Rmismatch=1,with.Rindels=TRUE) Error in solveUserSEW(width(x), start = start, end = end, width = width) : solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (0) is < 1
[2] how can i see the code of such functions: which.isMatchingStartingAt, rev, normargPattern which are called by Biostrings:::.computeTrimEnd showMethods("which.isMatchingStartingAt") can not work [3] max.Rmismatch=0.1 will be replaced by 0.1*nchar(Rpattern) and then by (-1,-1,...as.integer(0.1*nchar(Rpattern))) to better control each try, can i use max.Rmismatch=0.1*(1:nchar(Rpattern)) good luck shan gao [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing