Provided by: libbio-perl-perl_1.7.2-2_all bug

NAME - Haplotype tag object.


           use Bio::PopGen::TagHaplotype;

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


       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 module also on this folder.  In any case if, you provide an haplotype the module
       will try to find the answer to your question.


           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]


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AUTHOR - Pedro M. Gomez-Fabre

       Email pgf18872-at-gsk-dot-com

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

        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

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

        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

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

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

        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

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


                  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

        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 enough to define the haplotype set.
        Returns :
        Args    : none
        Status  : private