[Bioc-sig-seq] Minor bug in method 'aligned' of class 'PairwiseAlignedFixedSubject'

[Joern Toedling]

Hello,

I believe there is a minor bug in the visualization provided by the "aligned"
method of the class "PairwiseAlignedFixedSubject".
I performed a pairwise alignment looking for overlaps between reads and a
fixed subject DNAString. Here are 10 reads which all show some form overlap
with the subject.

> aligned(pa)
  A DNAStringSet instance of length 10
     width seq
 [1]    37 CTTTAGGCACCAT------------------------
 [2]    37 CTGTAGTCACCATC-----------------------
 [3]    37 CTGTAGGCACCATC-----------------------
 [4]    37 CTGTAGGCACCATC-----------------------
 [5]    37 CTGTAGGCACCATCAAT--------------------
 [6]    37 CTTTAGTCAACATC-----------------------
 [7]    37 CTGTAGG------------------------------
 [8]    37 CTGTAGGCACCATCAATCGT-----------------
 [9]    37 --------------------------------GCTTT
[10]    37 CTGTATTCACCATCAA---------------------
> start(pattern(pa))
 [1] 24 23 23 23 20 23 30 17  1 21
> end(pattern(pa))
 [1] 36 36 36 36 36 36 36 36  5 36

So in fact for 9 of the 10 reads the overlap is at the end of the read, and
for one at the start. However, the visualization of the "aligned" method
wrongly suggest that it is the other way round.

Regards,
Joern

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-18 r48561) 
i686-pc-linux-gnu 

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] ShortRead_1.3.5   lattice_0.17-25   BSgenome_1.13.2   Biostrings_2.13.9
[5] IRanges_1.3.16   

loaded via a namespace (and not attached):
[1] Biobase_2.5.2 grid_2.10.0   hwriter_1.1  


---
Joern Toedling
Institut Curie -- UMR218
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246942