NAME
    Mash

SYNOPSIS
    A module to read `mash info` output and transform it

      use strict;
      use warnings;
      use Mash;

      # Quick example

      # Sketch all fastq files into one mash file.
      system("mash sketch *.fastq.gz > all.msh");
      die if $?;
      # Read the mash file.
      my $msh = Mash->new("all.msh");
      # All-vs-all distances
      my $distHash = $msh->dist($msh);

DESCRIPTION
    This is a module to read mash files produced by the Mash executable. For
    more information on Mash, see mash.readthedocs.org. This module is
    capable of reading mash files. Future versions will read/write mash
    files.

METHODS
    Mash->new("filename.msh",\%options);
        Create a new instance of Mash. One object per set of files.

          Arguments:  Sketch filename
                      Hash of options (none so far)
          Returns:    Mash object

    $msh->file("filename.msh")
        Changes which file is used in the object and updates internal object
        information. This method is ordinarily used internally only.

          Arguments: One mash file
          Returns:   self

    $msh->dist($msh2)
        Returns a hash describing distances between sketches represented by
        this object and another object. If there are multiple sketches per
        object, then all sketches in this object will be compared against
        all sketches in the other object.

          Arguments: One Mash object
          Returns:   reference to a hash of hashes. Each value is a number.

        Aliases: distance(), mashDist()

    Mash::raw_mash_distance($array1, $array2)
        Returns the number of sketches in common and the total number of
        sketches between two lists. The return type is an array of two
        elements.

          Arguments: A list of integers
                     A list of integers
          Returns:   (countOfInCommon, totalNumber)

          Example:
    
            my $R1 = [1,2,3];
            my $R2 = [1,2,4];
            my($common, $total) = Mash::raw_mash_distance($R1,$R2);
            # $common => 2
            # $total  => 3

COPYRIGHT AND LICENSE
    MIT license.

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

    For additional help, go to https://github.com/lskatz/perl-mash

    CPAN module at http://search.cpan.org/~lskatz/perl-mash