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

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