R Under development (unstable) (2025-09-02 r88773 ucrt) -- "Unsuffered Consequences"
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> library(SVAlignR)
> data(longreads)
> seqs <- longreads$connection[1:15]
> pad <- c(rep("0", 9), rep("", 6))
> names(seqs) <- paste("LR", pad, 1:length(seqs), sep = "")
> seqs <- seqs[!duplicated(seqs)]
> 
> try( makeSubsMatrix(match = "13") )
Error in makeSubsMatrix(match = "13") : Both parameters must be numeric.

> try( makeSubsMatrix(mismatch = "13") )
Error in makeSubsMatrix(mismatch = "13") : 
  Both parameters must be numeric.

> 
> mysub <- makeSubsMatrix(match = 2, mismatch = -6)
> 
> ## test the 'alignCluster' method
> try( alignCluster(13) )
Error in strsplit(sampleText, split) : non-character argument
> 
> ab <- alignCluster(seqs, mysub)
use user defined matrix
> image(ab)
> 
> proc.time()
   user  system elapsed 
   2.60    0.39    2.98