Function
getKmerSimilarityMatrix
Creates a matrix storing the number of common q-grams between all pairs of sequences.
getKmerSimilarityMatrix(index, distMat[, seqSet])
Parameters
index
A q-gram index.
Types: Index_QGram
distMat
The resulting q-gram similarity matrix.
Types: Container
seqSet
Contains sequence numbers if only a subset of sequences should be compared.
Types: Container
Remarks
distMat will be resized to seqCount*seqCount, where seqCount is the number of sequences in the index/in seqSet. The number of common q-grams between sequence i and j is stored at position i*seqCount + j. It sums up the minimum number of q-gram occurrences between both sequences for each q-gram.
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