Implement k-mer subsetting methods #510
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This PR adds modern k-mer subsetting methods (e.g. minimizers and syncmers) to allow more rapid sequence matching:
MinimizerSelectorSyncmerSelectorCachedSyncmerSelectorMincodeSelectorThe implemented methods are based on finding the 'smallest' k-mer in a certain window. As the k-mer code itself would imply lexicographical sorting, different permutation schemes are implemented:
PermutationRandomPermutationFrequencyPermutationTo support the long k-mers that are typically used in modern read mapping methods, the
BucketKmerTableis introduced as memory-efficient twin of theKmerTable.Furthermore, an example is introduced that demonstrates gene counting using a combination of the new features.