On Sep 26, 2011, at 4:51 PM, wang peter wrote:
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
Let's hope this is the bug Herve mentioned yesterday, whose fix
should appear soon.
[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
> showMethods(which.isMatchingStartingAt, includeDefs=TRUE)
then
> Biostrings:::.matchPatternAt
rev is in base (see ?rev) [different from *reverse*, from IRanges]
> Biostrings:::normargPattern
[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))
Again, I can't tell what you're asking here.
good luck
shan gao
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