[Bioc-sig-seq] trimLRPatterns related error

[Kunbin Qu]

Hi, all,

I am trying to use trimLRPatterns to construct a set of reads after trimming from both ends. After trimming is done to the three prime, some reads are already down to zero. Then when I tried to trim from the five prime, the trimming (trimLRPatterns) did not raise any error, however, the following DNAStringSet construction threw some errors, like the following. Could anybody help me? Thanks a lot!

-Kunbin

> #after trimming from the five prime, read No. 2 now is zero in length
> seqsART
  A DNAStringSet instance of length 7
    width seq
[1]     5 NGTCA
[2]     0 
[3]     8 NCGGTGCA
[4]    24 NGACGGTTCACCCCTCGTGGGCAA
[5]    49 TATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA
[6]    36 TATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[7]    49 TATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAACCTAAACCAGGG
> trimCoordsAL<-trimLRPatterns(Lpattern=adapter, subject=seqsART, max.Lmismatch = rep(1,46), ranges=T, with.Lindels=TRUE)
> adapter<-DNAString("TTTACACGCGTCTCCCGGGCTTATCTCGTATGCCGTCTTCTGCTTG")
> trimCoordsAL
IRanges of length 7
    start end width
[1]     3   5     3
[2]     2   1     0
[3]     2   8     7
[4]     3  24    22
[5]    27  49    23
[6]    27  36    10
[7]    27  49    23
> seqsAL <- DNAStringSet(seqsART, start=start(trimCoordsAL), end=end(trimCoordsAL))
Error in solveUserSEW(width(x), start = start, end = end, width = width) : 
  solving row 2: 'allow.nonnarrowing' is FALSE and the supplied start (2) is > refwidth + 1
>

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