Bug: length of PairwiseAlignments

[gevro]

Hi,
Per the documentation, length should return the lengths of each alignment of a PairwiseAlignments object

General information methods
In the code snippets below, x is a PairwiseAlignments object, except otherwise noted.

alphabet(x): Equivalent to alphabet(unaligned(subject(x))).

length(x): The common length of alignedPattern(x) and alignedSubject(x). There is a method for PairwiseAlignmentsSingleSubjectSummary as well.

However, the latest version of Biostrings simply returns the total number of alignments within the PairwiseAlignments object.

I believe this is a bug. Also, there does not seem to be a function to do what the documentation indicates.

[hpages]

Hi,

However, the latest version of Biostrings simply returns the total number of alignments within the PairwiseAlignments object.

This has always been the case and is the expected behavior of length() on a PairwiseAlignments object:

library(Biostrings)
pattern <- AAStringSet(c("PAWHEAE", "PAWHAE", "PAWWHEAE"))
subject <- AAString("HEAGAWGHEE")
x <- pairwiseAlignment(pattern, subject)
x
length(x)
# [1] 3

Also I don't see any contradiction with the documentation:

alignedPattern(x)
# AAStringSet object of length 3:
#     width seq
# [1]    10 P---AWHEAE
# [2]    10 P---AW-HAE
# [3]    11 P---AWWHEAE

length(alignedPattern(x))
# [1] 3

alignedSubject(x)
# AAStringSet object of length 3:
#     width seq
# [1]    10 HEAGAWGHEE
# [2]    10 HEAGAWGHEE
# [3]    11 HEAGAWGHE-E

length(alignedSubject(x))
# [1] 3

Use nchar() if you want the lengths of each alignment in the PairwiseAlignments object:

nchar(x)
# [1] 10 10 11

[gevro]

Ok thank you.