Hi all,
I'm trimming reads using an Rpattern which in some cases extends on the
left side. If the pattern starts at exactly position -1 trimLRPattern
throws an error. If the pattern starts further 'upstream' it returns a
zero length sequence, as expected:
library(ShortRead)
# create a pattern
fragment <- paste(sample(c('A','C','G','T'),10,replace=TRUE),collapse='')
# create some reads based on the pattern; for different reads the
# pattern extends either on the left, the right, or both sides
reads <- substring(fragment,1:4,7:10)
# trim all reads; all reads should match the pattern fully and be
# trimmed from start to end
trimLRPatterns(Rpattern=fragment, subject=DNAStringSet(reads),
max.Rmismatch=0.5, ranges=TRUE, Rfixed=FALSE)
# IRanges of length 4
# start end width
# [1] 1 0 0
# [2] 0 -1 0
# [3] -1 -2 0
# [4] -2 -3 0
# if I want the reads to be trimmed right away an error is thrown for
# the second read
trimLRPatterns(Rpattern=fragment, subject=DNAStringSet(reads[c(1,3,4)]),
max.Rmismatch=0.5, ranges=FALSE)
# A DNAStringSet instance of length 3
# width seq
# [1] 0
# [2] 0
# [3] 0
trimLRPatterns(Rpattern=fragment, subject=DNAStringSet(reads[2]),
max.Rmismatch=0.5, ranges=FALSE)
# 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
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.8.2 Rsamtools_1.2.1 lattice_0.19-13
[4] Biostrings_2.18.2 GenomicRanges_1.2.2 IRanges_1.8.7
[7] multtest_2.6.0 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] grid_2.12.0 hwriter_1.3 MASS_7.3-9 splines_2.12.0
[5] survival_2.36-2 tools_2.12.0
Where is this error coming from?
Ludo
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