Edit distances between reads and a small number of short references
srdistance calculates the edit distance from each read in
pattern to each read in
subject. The underlying
pairwiseAlignment is only efficient when both
reads are short, and when the number of
subject reads is small.
An object of class
additional arguments, unused.
The underlying algorithm performs pairwise alignment from each read in
pattern to each sequence in
subject. The return value is
a list of numeric vectors of distances, one list element for each
subject. The vector in each list element contains
for each read in
pattern the edit distance from the read to the
corresponding subject. The weight matrix and gap penalties used to
calculate the distance are structured to weight base substitutions and
single base insert/deletions equally. Edit distance between known and
ambiguous (e.g., N) nucleotides, or between ambiguous nucleotides, are
weighted as though each possible nucleotide in the ambiguity were
A list of length equal to that of
subject. Each element is a
numeric vector equal to the length of
pattern, with values
corresponding to the minimum distance between between the
corresponding pattern and subject sequences.
Martin Morgan <firstname.lastname@example.org>
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