NAME

       Bio::PopGen::TagHaplotype.pm - Haplotype tag object.

SYNOPSIS

           use Bio::PopGen::TagHaplotype;

           my $obj = Bio::PopGen::TagHaplotype -> new($hap);

DESCRIPTION

       This module take as input a haplotype and try toe get the minimal set of SNP that define
       the haplotype. This module can be use alone.  But due to the tagging haplotype process is
       exponential one. My suggestion is that before to use this module you pass your data under
       Select.mp module also on this folder.  In any case if, you provide an haplotype the module
       will try to find the answer to your question.

CONSTRUCTORS

           my $obj = Bio::PopGen::TagHaplotype -> new($hap);

           were $hap is the reference to an array of array with the haplotype.

           $hap= [[0, 0, 0],
                  [1, 0, 0],
                  [0, 1, 1]
                 ];

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Pedro M. Gomez-Fabre

       Email pgf18872-at-gsk-dot-com

   new
        Title   : new
        Function: constructor of the class.
        Returns : self hash
        Args    : input haplotype (array of array)
        Status  : public

   haplotype_block
        Title   : haplotype_block
        Usage   : my $haplotype_block = $TagHaplotype->haplotype_block();
        Function: Get the haplotype block for a haplotype tagging selection
        Returns : reference of array
        Args    : reference of array with haplotype pattern

   input_block
        Title   : input_block
        Usage   : $obj->input_block()
        Function: returns haplotype block. By now will produce the same output than
                  $self->haplotype_block. but for compatiblity, this method is kept.
                  This method is deprecated.
        Returns : reference to array of array with the haplotype input value
        Args    : none
        Status  : public

   tag_list
        Title   : tag_list
        Usage   : $obj->tag_list()
        Function: returns the list of SNPs combination that identify the
                  haplotype. All combinations are displayed as arrays
        Returns : reference to array of array.
        Args    : none
        Status  : public

   tag_length
        Title   : tag_length
        Usage   : $obj->tag_length()
        Function: returns the length of the tag.
        Returns : scalar
        Args    : none
        Status  : public

   _scan_snp
        Title   : _scan_snp
        Usage   : internal
        Function: scan sets increasing the length until find a non degenerated
                  pattern.
        Returns : scalar
        Args    : none
        Status  : private

   _gen_comb
        Title   : _gen_comb
        Usage   : internal
        Function: we supply the length of the haplotype and the length of the
                  word we need to find and the functions returns the possible
                  list of combinations.
        Returns : scalar
        Args    : none
        Status  : private

   _generateCombinations
        Title   : _generateCombinations
        Usage   : internal
        Function: Recursive function that produce all combinations for a set

                  i.e.:

                  1, 2, 3, 4

                  and word of B<3> will produce:

                  1, 2, 3
                  1, 2, 4
                  1, 3, 4
                  2, 3, 4

        Returns :
        Args    : none
        Status  : private

   _scan_combinations
        Title   : _scan_combinations
        Usage   : internal
        Function: take the haplotype and a list of possible combination
                  for that length. Generate a subset and scan it to find if
                  the information is enought to define the haplotype set.
        Returns :
        Args    : none
        Status  : private