NAME
    Bio::Kmer

SYNOPSIS
    A module for helping with kmer analysis.

      use strict;
      use warnings;
      use Bio::Kmer;
  
      my $kmer=Bio::Kmer->new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});
      my $kmerHash=$kmer->kmers();
      my $countOfCounts=$kmer->histogram();

DESCRIPTION
    A module for helping with kmer analysis. The basic methods help count
    kmers and can produce a count of counts. Currently this module only
    supports fastq format. Although this module can count kmers with pure
    perl, it is recommended to give the option for a different kmer counter
    such as Jellyfish.

METHODS
    Bio::Kmer->new($filename, \%options)
        Create a new instance of the kmer counter. One object per file.

          Applicable arguments:
          Argument     Default    Description
          kmercounter  perl       What kmer counter software to use.
                                  Choices: Perl, Jellyfish.
          kmerlength   21         Kmer length
          numcpus      1          This module uses perl 
                                  multithreading with pure perl or 
                                  can supply this option to other 
                                  software like jellyfish.
          gt           1          If the count of kmers is fewer 
                                  than this, ignore the kmer. This 
                                  might help speed analysis if you 
                                  do not care about low-count kmers.

          Examples:
          my $kmer=Bio::Kmer->new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});

    $kmer->query($queryString)
        Query the set of kmers with your own query

          Arguments: query (string)
          Returns:   Count of kmers. 
                      0 indicates that the kmer was not found.
                     -1 indicates an invalid kmer (e.g., invalid length)

    $kmer->histogram()
        Count the frequency of kmers.

          Arguments: none
          Returns:   Reference to an array of counts. The index of 
                     the array is the frequency.

    $kmer->union($kmer2)
        Count the frequency of kmers.

          Arguments: Another Bio::Kmer object
          Returns:   List of kmers

    $kmer->union($kmer2)
        Count the frequency of kmers.

          Arguments: Another Bio::Kmer object
          Returns:   List of kmers

COPYRIGHT AND LICENSE
    MIT license. Go nuts.

AUTHOR
    Author: Lee Katz <lkatz@cdc.gov>

    For additional help, go to https://github.com/lskatz/Bio--Kmer

