context('Alignment')
test_that('The aligner works', {
seqs <- DNAStringSet(rep(paste(rep('A', 50), collapse=""), 5))
aligned <- align_sequences(seqs)
expect_that(all(seqs == unname(aligned)), is_true())
seqs <- DNAStringSet(c('AAAAAAAAAAATGAAACGTTAGCGCGTTTTTTTTTT',
'AAAAAAAAAAATGCGTTAGCGCGTTTTTTTTTT'))
aligned <- align_sequences(seqs)
target <- DNAStringSet(c('AAAAAAAAAAATGAAACGTTAGCGCGTTTTTTTTTT',
'AAAAAAAAAAATG---CGTTAGCGCGTTTTTTTTTT'))
expect_that(all(target == aligned), is_true())
})
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