# fn() countKmers
Counts kmers in a sequence. Optionally, a background model is returned.

Defined in | <seqan/alignment_free.h>
Signature | `void countKmers(kmerCounts, sequence, k); void countKmers(kmerCounts, bgFrequencies, sequence, k); void countKmers(kmerCounts, bgModel, sequence, k);`

## Parameters

`kmerCounts` | String of `unsigned` with kmer counts for every k-mer.
`bgFrequencies` | String of background frequencies (`double`) representing the model.
`bgModel` | MarkovModel to use.
`sequence` | String (sequence) where k-mers are counted.
`k` | k-mer length (`unsigned`).

## Detailed Description

k-mers overlapping masked (aka 'N') letters are not counted in case of Dna5Strings. A Bernoulli or Markov Model can be choosen as a background model.

### Examples

Calculate the alignment free sequence similarity o two masked DNA sequences.

    using namespace seqan;
    // Masked sequence, we do not want to count words overlapping 'N'
    Dna5String sequenceDna5 =
        "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
        "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
        "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
        "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
        "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
        "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
        "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";

    String<unsigned> kmerCounts;
    unsigned k = 2;  // Count all 2-mers
    countKmers(kmerCounts, sequenceDna5, k);

    for(unsigned i = 0; i<16; ++i)       // Print the 2-mer counts
        std::cout<<kmerCounts[i]<<"\n";  // 34 times AA; 30 times AC; 28 times AG; ...

    String<double> nucleotideFrequencies;  // Defines a Bernoulli model for DNA sequences.
    // Count all 2-mers and save the nucleotide frequencies
    countKmers(kmerCounts, nucleotideFrequencies, sequenceDna5, k);

    for(unsigned i = 0; i<4; ++i)          // Print the nucleotide frequencies
        std::cout << nucleotideFrequencies[i] << "\n";
    // => p(A) = 0.238; p(C) = 0.254; p(G) = 0.238; p(T) = 0.27;

    MarkovModel<Dna, double>  backgroundModel(1);  // Markov model of order 1
    // Count all 2-mers and return a Markov model
    countKmers(kmerCounts, backgroundModel, sequenceDna5, k);
    std::cout<<backgroundModel.transition;  // Print the transition matrix of the markov model

## Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## See Also

- MarkovModel
- alignmentFreeComparison
- calculateCovariance
- calculateProbability
- calculateVariance
- stringToStringSet

#### Dox Sources

    /*!
     * @fn countKmers
     *
     * @headerfile <seqan/alignment_free.h>
     *
     * @brief Counts kmers in a sequence. Optionally, a background model is
     *        returned.
     *
     * @signature void countKmers(kmerCounts, sequence, k);
     * @signature void countKmers(kmerCounts, bgFrequencies, sequence, k);
     * @signature void countKmers(kmerCounts, bgModel, sequence, k);
     *
     * @param[out] kmerCounts @link String @endlink of <tt>unsigned</tt> with kmer
     *                        counts for every k-mer.
     * @param[out] bgFrequencies @link String @endlink of background frequencies
     *                           (<tt>double</tt>) representing the model.
     * @param[out] bgModel @link MarkovModel @endlink to use.
     * @param[in] sequence @link String @endlink (sequence) where k-mers are
     *                     counted.
     * @param[in] k k-mer length (<tt>unsigned</tt>).
     *
     * k-mers overlapping masked (aka 'N') letters are not counted in case of
     * Dna5Strings. A Bernoulli or Markov Model can be choosen as a background
     * model.
     *
     * @section Examples
     *
     * Calculate the alignment free sequence similarity o two masked DNA sequences.
     *
     * @code{.cpp}
     * using namespace seqan;
     * // Masked sequence, we do not want to count words overlapping 'N'
     * Dna5String sequenceDna5 =
     *     "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
     *     "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
     *     "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
     *     "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
     *     "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
     *     "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
     *     "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
     *
     * String<unsigned> kmerCounts;
     * unsigned k = 2;  // Count all 2-mers
     * countKmers(kmerCounts, sequenceDna5, k);
     *
     * for(unsigned i = 0; i<16; ++i)       // Print the 2-mer counts
     *     std::cout<<kmerCounts[i]<<"\n";  // 34 times AA; 30 times AC; 28 times AG; ...
     *
     *
     * String<double> nucleotideFrequencies;  // Defines a Bernoulli model for DNA sequences.
     * // Count all 2-mers and save the nucleotide frequencies
     * countKmers(kmerCounts, nucleotideFrequencies, sequenceDna5, k);
     *
     * for(unsigned i = 0; i<4; ++i)          // Print the nucleotide frequencies
     *     std::cout << nucleotideFrequencies[i] << "\n";
     * // => p(A) = 0.238; p(C) = 0.254; p(G) = 0.238; p(T) = 0.27;
     *
     * MarkovModel<Dna, double>  backgroundModel(1);  // Markov model of order 1
     * // Count all 2-mers and return a Markov model
     * countKmers(kmerCounts, backgroundModel, sequenceDna5, k);
     * std::cout<<backgroundModel.transition;  // Print the transition matrix of the markov model
     * @endcode
     *
     *
     * @see alignmentFreeComparison
     * @see calculateProbability
     * @see calculateVariance
     * @see calculateCovariance
     * @see stringToStringSet
     * @see MarkovModel
     */