=pod

=head1 NAME

Bio::Kmer

=head1 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();

=head1 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.

=pod

=head1 METHODS

=over

=item 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});

=back


=cut

=pod

=over

=item $kmer->query($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)

=back


=cut

=pod

=over

=item $kmer->histogram()

Count the frequency of kmers.

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

=back


=cut

=pod

=over

=item $kmer->union($kmer2)

Count the frequency of kmers.

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

=back


=cut

=pod

=over

=item $kmer->union($kmer2)

Count the frequency of kmers.

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

=back


=cut

=pod

=head1 COPYRIGHT AND LICENSE

MIT license.  Go nuts.

=head1 AUTHOR

Author: Lee Katz <lkatz@cdc.gov>

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


=cut

