A toolkit for working with phylogenetic data.
v0.18.0
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signatures.hpp File Reference
#include <string>
#include <vector>

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Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::sequence
 

Functions

std::vector< size_t > kmer_counts (Sequence const &seq, size_t k)
 Count the occurences of k-mers of size k, for nucleic acids "ACGT". More...
 
std::vector< size_t > kmer_counts (Sequence const &seq, size_t k, std::string const &alphabet)
 Count the occurences of k-mers of size k, for a given alphabet. More...
 
std::vector< std::string > kmer_list (size_t k, std::string const &alphabet)
 Return the list of all possible k-mers for a given k and alphabet. More...
 
std::vector< size_t > kmer_reverse_complement_indices (size_t k)
 Get a map from indices of kmer_list() and kmer_counts() vectors to a smaller list of size kmer_reverse_complement_size() which combines reverse complementary kmers. More...
 
size_t kmer_reverse_complement_size (size_t k)
 Get the size needed to store reverse complement kmers. More...
 
std::string reverse_complement (std::string const &sequence)
 Get the reverse complement of a sequences of ACGT characters. More...
 
std::vector< double > signature_frequencies (Sequence const &seq, size_t k)