Closed jergosh closed 5 years ago
Hi @jergosh,
This was only the show()
method not displaying the entire thing to save screen space (admittedly a questionable feature). But calling writePairwiseAlignments()
on the object returned by pairwiseAlignment()
would have showed you that the alignment is correct.
Anyway the show()
method was fixed a while ago in Biostrings:
> pairwiseAlignment(pattern="succeed", subject="supersede", gapOpening=0, gapExtension=1)
Global PairwiseAlignmentsSingleSubject (1 of 1)
pattern: su-cce--ed-
subject: sup--ersede
score: 7.945507
Sorry for the slow answer.
Best, H.
> sessionInfo()
R version 3.6.0 Patched (2019-05-02 r76454)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.6.r76454/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.6.r76454/lib/libRlapack.so
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=en_US.UTF-8 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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Biostrings_2.53.2 XVector_0.25.0 IRanges_2.19.17
[4] S4Vectors_0.23.25 BiocGenerics_0.31.6
loaded via a namespace (and not attached):
[1] zlibbioc_1.31.0 compiler_3.6.0 tools_3.6.0
It appears that pairwiseAligment behaves as if it was always performing local alignment, no matter what value I set in the
type
parameter. Just taking the example from https://www.bioconductor.org/packages/3.7/bioc/vignettes/Biostrings/inst/doc/PairwiseAlignments.pdfwhat I'm getting:
whereas the expected result (taken from the pdf I linked) would be:
My session info:
Many thanks, Greg