Hi,

I am getting an error when using writePairwiseAlignments to align a specific pair DNA sequences. They are similar, but one has an approximately 10 bp long indel. Here are the commands I am running and their output:

> pa <- PairwiseAlignments(pattern = "CGWACATCACCATCCCTGGATCTCATTCCAAACATTCACAGTCACTGAGCAGCAGCAATGACTGAGATTTTAGAGGAGCGGCCTTTCGGCTCTAATACCAACGTCTACTTATCAATTTTCGTACTTTTTTGCTTTAAACTTTTTGTCAAGATTAGCTTGAACATACTTACTCACTTCTACGTGGTTAAAGGAAATCGTAAGGAAGCAGCACGGATCGCAGCTGAGTTCTATGATTTTGCCCAAGGGCACAGTAAGTAGGCACACATTGTGGTTATTTATTTTGGAGTCTGTTTTGTTGTGTCTGTATATAAATATCACTGTTAAATATTTTACTTGTTTTACAGGGAGTAAAAGAGAAAGTGTCTGTTGCATGGCCCARTTTGTAACCA", subject = "CGWACATCACCATCCCTGAATCTCATTCCAAACATTCACAGTCACTGAGCAGCAGCAATGACTGAGATTTTAGAGGAGCGGCCTTTCGGCTCTAATACCAATGTCTACTTATCAATTTTCGTACTTTTTTGCTTTAAACTTTTTGTCAAGATTAGCTTGAACATACTTACTCACACAAAGGAAATCGTAAGGAAGCAGCACGGATCGCAGCTGAGTTCTATGATTTTGGCCAAGGGCACRGTAAGTAGGCACACGTTGTGGCTATTTATTTCGGAGTCTGTTTTGTTGTGTCTGTATATAAATGTCTCTGGTATATATTTGACTTGTTTTACCGGGAGTAAAAGAGAAAGTGTCTGTTGCATGGCCCAGTTTGTAACCRTTTGTAACCA", gapExtension = 0, type = "global")
> writePairwiseAlignments(pa)

########################################
# Program: Biostrings (version 2.36.1), a Bioconductor package
# Rundate: Wed Jun  3 15:49:00 2015
########################################
Error in .makePipes(x) : 
  Biostrings internal error: mismatches and/or indels reported in 'pattern(x)' and 'subject(x)' are inconsistent

What could be causing this?

Thanks,

Jonathon

> sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] BiocInstaller_1.18.2 sangerseqR_1.4.0     Biostrings_2.36.1    XVector_0.8.0        IRanges_2.2.3       
[6] BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6     digest_0.6.8    mime_0.3        R6_2.0.1        xtable_1.7-4    stats4_3.2.0   
 [7] zlibbioc_1.14.0 RUnit_0.4.28    tools_3.2.0     shiny_0.12.0    httpuv_1.3.2    htmltools_0.2.6

Hi Jonathon,

You need to call pairwiseAlignment() and not PairwiseAlignments() to perform pairwise alignments. PairwiseAlignments() does not perform any alignment: it's just a low-level constructor for stuffing a PairwiseAlignments object "by hand". Maybe it should not be exposed since the end-user almost never needs to call it directly.

Cheers,

H.