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Is it possible to set the 'match' and 'mismatch' scores? #1

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mantzaris opened this issue Sep 21, 2020 · 2 comments
Closed

Is it possible to set the 'match' and 'mismatch' scores? #1

mantzaris opened this issue Sep 21, 2020 · 2 comments

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@mantzaris
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Using bb = align(read = "AAAA", reference = "AAAA")

then the score produced via: bb$alignment$optimal_score is 8. It seems that the match score is set to 2. Is it possible to set it to 1? Also is it possible to set the 'mismatch score'? The other score values and the start and stop are understood how they can be edited via align(read = "AAAA", reference = "AAAA", gap_open = 5L, gap_extension = 2L, start_idx = 0L, end_idx = 0L)
@nanxstats
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Fixed in 53b1c5e. Please try it out.

@mantzaris
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Works perfectly, thank you for the modification

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@nanxstats @mantzaris