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.\" ========================================================================
.\"
.IX Title "Bio::PopGen::TagHaplotype 3pm"
.TH Bio::PopGen::TagHaplotype 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::PopGen::TagHaplotype.pm \- Haplotype tag object.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Bio::PopGen::TagHaplotype;
\&
\&    my $obj = Bio::PopGen::TagHaplotype \-> new($hap);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module take as input a haplotype and try toe get the minimal set
of \s-1SNP\s0 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.
.SH "CONSTRUCTORS"
.IX Header "CONSTRUCTORS"
.Vb 1
\&    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]
\&          ];
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Pedro M. Gomez-Fabre"
.IX Header "AUTHOR - Pedro M. Gomez-Fabre"
Email pgf18872\-at\-gsk\-dot\-com
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Function: constructor of the class.
\& Returns : self hash
\& Args    : input haplotype (array of array)
\& Status  : public
.Ve
.SS "haplotype_block"
.IX Subsection "haplotype_block"
.Vb 5
\& 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
.Ve
.SS "input_block"
.IX Subsection "input_block"
.Vb 8
\& 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
.Ve
.SS "tag_list"
.IX Subsection "tag_list"
.Vb 7
\& 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
.Ve
.SS "tag_length"
.IX Subsection "tag_length"
.Vb 6
\& Title   : tag_length 
\& Usage   : $obj\->tag_length()
\& Function: returns the length of the tag.
\& Returns : scalar 
\& Args    : none
\& Status  : public
.Ve
.SS "_scan_snp"
.IX Subsection "_scan_snp"
.Vb 7
\& Title   : _scan_snp 
\& Usage   : internal
\& Function: scan sets increasing the length until find a non degenerated
\&           pattern. 
\& Returns : scalar
\& Args    : none
\& Status  : private
.Ve
.SS "_gen_comb"
.IX Subsection "_gen_comb"
.Vb 8
\& 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
.Ve
.SS "_generateCombinations"
.IX Subsection "_generateCombinations"
.Vb 3
\& 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
.Ve
.SS "_scan_combinations"
.IX Subsection "_scan_combinations"
.Vb 8
\& 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
.Ve