annotate variant_effect_predictor/Bio/EnsEMBL/Variation/ReadCoverageCollection.pm @ 1:d6778b5d8382 draft default tip

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author willmclaren
date Fri, 03 Aug 2012 10:05:43 -0400
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0
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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 # Ensembl module for Bio::EnsEMBL::Variation::ReadCoverage
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22 #
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23 # Copyright (c) 2008 Ensembl
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24 #
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25
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26
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27 =head1 NAME
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28
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29 Bio::EnsEMBL::Variation::ReadCoverageCollection - A collection of coverage reagion for a read.
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30
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31 =head1 SYNOPSIS
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32
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33 # Read coverage collection feature representing a genomic region covered by a read
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34
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35 $rcc = Bio::EnsEMBL::Variation::ReadCoverageCollection->new
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36 (-start => 100,
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37 -end => 200,
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38 -strand => 1,
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39 -slice => $slice,
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40 -window_start => 1,
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41 -window_end => 1000,
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42 -window_size => 50,
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43 -read_coverage_avg => 100,
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44 -read_coverage_min => 0,
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45 -read_coverage_max => 200,
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46 -sample => $individual);
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47
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48
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49 print $rcc->start(), "-", $rcc->end(), "\n";
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50
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51
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52 =head1 DESCRIPTION
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53
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54 This is a class representing the read coverage collection information
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55 from the ensembl-variation database. A ReadCoverageCollection behaves as any other Ensembl feature collection.
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56 Object for storing read_coverage scores. The scores are averaged (also the minimum and maximum scores) over different window sizes to speed up drawing over large regions. The scores are packed as integer and stored in a string
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57 See B<Bio::EnsEMBL::Feature>.
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58
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59 =head1 METHODS
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60
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61 =cut
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62
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63 use strict;
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64 use warnings;
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65
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66 package Bio::EnsEMBL::Variation::ReadCoverageCollection;
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67
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68 use Bio::EnsEMBL::Feature;
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69 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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70 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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71
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72 our @ISA = ('Bio::EnsEMBL::Feature');
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73
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74
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75 =head2 new
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76
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77 Arg [-ADAPTOR] :
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78 see superclass constructor
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79 Arg [-START] :
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80 start relative to the slice,see superclass constructor
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81 Arg [-END] :
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82 end relative to the slice,see superclass constructor
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83 Arg [-STRAND] :
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84 1 or -1, same as strand for the slice,see superclass constructor
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85 Arg [-SLICE] :
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86 see superclass constructor
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87 Arg [-SEQ_REGION_START] :
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88 start relative to chromosome,see superclass constructor
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89 Arg [-SEQ_REGION_END] :
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90 end relative to chromosome,see superclass constructor
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91 Arg [-SEQ_REGION_STRAND] :
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92 always 1, see superclass constructor
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93 int Arg [-SCORE_MIN] :
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94 average read_coverage for a window
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95 Arg [-SCORE_AVG] :
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96 minimum read_coverage for a window
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97 Arg [-SCORE_MAX] :
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98 maximum read_coverage for a window
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99 Arg [-SAMPLE_ID] :
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100 int - the individual in which the read_covarage is recorded
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101
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102 Example :
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103 $rc = Bio::EnsEMBL::Variation::ReadCoverage->new
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104 (-start => 100,
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105 -end => 100,
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106 -slice => $slice,
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107 -window_size => 50,
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108 -sample_id => 1);
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109
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110 Description: Constructor. Instantiates a new ReadCoverageCollection object.
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111 Returntype : Bio::EnsEMBL::Variation::ReadCoverageCollection
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112 Exceptions : none
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113 Caller : general
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114 Status : At Risk
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115
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116 =cut
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117
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118 sub new {
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119 my $caller = shift;
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120 my $class = ref($caller) || $caller;
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121
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122 my $self = $class->SUPER::new(@_);
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123 my ($window_size,$window_start,$window_end,$sample_id,$read_coverage_avg,$read_coverage_min,$read_coverage_max,$y_axis_min,$y_axis_max) =
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124 rearrange([qw(WINDOW_SIZE WINDOW_START WINDOW_END SAMPLE_ID READ_COVERAGE_AVG READ_COVERAGE_MIN READ_COVERAGE_MAX Y_AXIS_MIN Y_AXIS_MAX)], @_);
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125
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126 $self->{'window_size'} = $window_size;
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127 $self->{'window_start'} = $window_start;
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128 $self->{'window_end'} = $window_end;
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129 $self->{'sample_id'} = $sample_id;
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130 $self->{'read_coverage_avg'} = $read_coverage_avg;
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131 $self->{'read_coverage_min'} = $read_coverage_min;
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132 $self->{'read_coverage_max'} = $read_coverage_max;
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133 $self->{'y_axis_min'} = $y_axis_min;
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134 $self->{'y_axis_max'} = $y_axis_max;
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135 return $self;
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136 }
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137
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138 =head new_fast
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139
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140 Arg [1] : hash reference $hashref
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141 Example : none
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142 Description: This is an ultra fast constructor which requires knowledge of
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143 the objects internals to be used.
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144 Returntype :
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145 Exceptions : none
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146 Caller :
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147
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148 sub new_fast {
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149
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150 my ($class, $hashref) = @_;
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151
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152 return bless $hashref, $class;
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153
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154 }
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155
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156 =head2 window_size
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157
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158 Arg[1] : int $newval (optional)
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159 The new value to set the window_size attribute to
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160 Example : $window_size = $obj->window_size();
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161 Description : Getter/Setter for the window_size attribute.
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162 the window size this feature has been seen in the genome
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163 ReturnType : int
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164 Exceptions : none
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165 Caller : general
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166 Status : At Risk
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167
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168 =cut
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169
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170 sub window_size{
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171 my $self = shift;
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172 return $self->{'window_size'} = shift if (@_);
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173 return $self->{'window_size'};
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174 }
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175
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176 =head2 window_start
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177
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178 Arg[1] : int $newval (optional)
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179 The new value to set the window_start attribute to
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180 Example : $window_start = $obj->window_start();
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181 Description : Getter/Setter for the window_start attribute.
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182 the window start this feature has been seen in the genome
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183 ReturnType : int
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184 Exceptions : none
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185 Caller : general
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186 Status : At Risk
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187
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188 =cut
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189
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190 sub window_start{
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191 my $self = shift;
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192 return $self->{'window_start'} = shift if (@_);
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193 return $self->{'window_start'};
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194 }
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195
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196 =head2 window_end
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197
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198 Arg[1] : int $newval (optional)
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199 The new value to set the window_end attribute to
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200 Example : $depth = $obj->window_end();
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201 Description : Getter/Setter for the window_end attribute.
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202 the window end this feature has been seen in the genome
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203 ReturnType : int
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204 Exceptions : none
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205 Caller : general
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206 Status : At Risk
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207
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208 =cut
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209
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210 sub window_end{
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211 my $self = shift;
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212 return $self->{'window_end'} = shift if (@_);
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213 return $self->{'window_end'};
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214 }
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215
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216 =head2 read_coverage_avg
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217
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218 Arg[1] : int $newval (optional)
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parents:
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219 The new value to set the read_coverage_avg attribute to
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willmclaren
parents:
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220 Example : $avg = $obj->read_coverage_avg();
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willmclaren
parents:
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221 Description : Getter/Setter for the score_avg attribute.
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willmclaren
parents:
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222 the average read_coverage this feature has
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willmclaren
parents:
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223 ReturnType : int
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willmclaren
parents:
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224 Exceptions : none
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willmclaren
parents:
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225 Caller : general
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willmclaren
parents:
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226 Status : At Risk
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willmclaren
parents:
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227
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willmclaren
parents:
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228 =cut
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willmclaren
parents:
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229
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willmclaren
parents:
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230 sub read_coverage_avg{
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willmclaren
parents:
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231 my $self = shift;
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willmclaren
parents:
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232 return $self->{'read_coverage_avg'} = shift if (@_);
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willmclaren
parents:
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233 return $self->{'read_coverage_avg'};
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willmclaren
parents:
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234 }
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willmclaren
parents:
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235
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willmclaren
parents:
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236 =head2 read_coverage_min
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willmclaren
parents:
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237
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willmclaren
parents:
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238 Arg[1] : int $newval (optional)
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willmclaren
parents:
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239 The new value to set the read_coverage_min attribute to
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willmclaren
parents:
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240 Example : $min = $obj->read_coverage_min();
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willmclaren
parents:
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241 Description : Getter/Setter for the score_min attribute.
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willmclaren
parents:
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242 the minimum read_coverage this feature has
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willmclaren
parents:
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243 ReturnType : int
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willmclaren
parents:
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244 Exceptions : none
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willmclaren
parents:
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245 Caller : general
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willmclaren
parents:
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246 Status : At Risk
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willmclaren
parents:
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247
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willmclaren
parents:
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248 =cut
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willmclaren
parents:
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249
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willmclaren
parents:
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250 sub read_coverage_min{
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willmclaren
parents:
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251 my $self = shift;
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willmclaren
parents:
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252 return $self->{'read_coverage_min'} = shift if (@_);
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willmclaren
parents:
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253 return $self->{'read_coverage_min'};
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willmclaren
parents:
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254 }
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willmclaren
parents:
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255
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willmclaren
parents:
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256 =head2 read_coverage_max
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willmclaren
parents:
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257
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willmclaren
parents:
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258 Arg[1] : int $newval (optional)
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willmclaren
parents:
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259 The new value to set the read_coverage_max attribute to
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willmclaren
parents:
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260 Example : $max = $obj->read_coverage_max();
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willmclaren
parents:
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261 Description : Getter/Setter for the read_coverage_max attribute.
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willmclaren
parents:
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262 the maximum read_coverage this feature has
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willmclaren
parents:
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263 ReturnType : int
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willmclaren
parents:
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264 Exceptions : none
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willmclaren
parents:
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265 Caller : general
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willmclaren
parents:
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266 Status : At Risk
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willmclaren
parents:
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267
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willmclaren
parents:
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268 =cut
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willmclaren
parents:
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269
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willmclaren
parents:
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270 sub read_coverage_max{
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willmclaren
parents:
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271 my $self = shift;
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willmclaren
parents:
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272 return $self->{'read_coverage_max'} = shift if (@_);
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willmclaren
parents:
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273 return $self->{'read_coverage_max'};
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willmclaren
parents:
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274 }
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willmclaren
parents:
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275
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willmclaren
parents:
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276
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willmclaren
parents:
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277 =head2 sample_id
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willmclaren
parents:
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278
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willmclaren
parents:
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279 Arg[1] : int $newval (optional)
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willmclaren
parents:
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280 The new value to set the sample_id attribute to
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willmclaren
parents:
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281 Example : $sample_id = $obj->sample_id();
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willmclaren
parents:
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282 Description : Getter/Setter for the individual dbId attribute.
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willmclaren
parents:
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283 the individual dbId this feature has been seen in the genome
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willmclaren
parents:
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284 ReturnType : int
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willmclaren
parents:
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285 Exceptions : none
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willmclaren
parents:
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286 Caller : general
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willmclaren
parents:
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287 Status : At Risk
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willmclaren
parents:
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288
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willmclaren
parents:
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289 =cut
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willmclaren
parents:
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290
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willmclaren
parents:
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291 sub sample_id{
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willmclaren
parents:
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292 my $self = shift;
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willmclaren
parents:
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293 return $self->{'sample_id'} = shift if (@_);
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willmclaren
parents:
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294 return $self->{'sample_id'};
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willmclaren
parents:
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295 }
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willmclaren
parents:
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296
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willmclaren
parents:
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297 =head2 y_axis_min
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willmclaren
parents:
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298
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willmclaren
parents:
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299 Arg[1] : int $newval (optional)
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willmclaren
parents:
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300 The new value to set the y_axiss_min attribute to
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willmclaren
parents:
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301 Example : $y_axis_min = $obj->y_axis_min();
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willmclaren
parents:
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302 Description : Getter/Setter for the minimum of read_coverage for the collection of feature.
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willmclaren
parents:
diff changeset
303
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willmclaren
parents:
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304 ReturnType : int
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willmclaren
parents:
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305 Exceptions : none
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willmclaren
parents:
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306 Caller : general
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willmclaren
parents:
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307 Status : At Risk
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willmclaren
parents:
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308
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willmclaren
parents:
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309 =cut
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willmclaren
parents:
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310
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willmclaren
parents:
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311 sub y_axis_min{
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willmclaren
parents:
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312 my $self = shift;
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willmclaren
parents:
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313 return $self->{'y_axis_min'} = shift if (@_);
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willmclaren
parents:
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314 return $self->{'y_axis_min'};
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willmclaren
parents:
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315 }
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willmclaren
parents:
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316
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willmclaren
parents:
diff changeset
317 =head2 y_axis_max
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willmclaren
parents:
diff changeset
318
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willmclaren
parents:
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319 Arg[1] : int $newval (optional)
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willmclaren
parents:
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320 The new value to set the y_axiss_max attribute to
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willmclaren
parents:
diff changeset
321 Example : $y_axis_max = $obj->y_axis_max();
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willmclaren
parents:
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322 Description : Getter/Setter for the maximum of read_coverage for the collection of feature.
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willmclaren
parents:
diff changeset
323
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willmclaren
parents:
diff changeset
324 ReturnType : int
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willmclaren
parents:
diff changeset
325 Exceptions : none
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willmclaren
parents:
diff changeset
326 Caller : general
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willmclaren
parents:
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327 Status : At Risk
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willmclaren
parents:
diff changeset
328
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willmclaren
parents:
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329 =cut
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willmclaren
parents:
diff changeset
330
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willmclaren
parents:
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331 sub y_axis_max{
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willmclaren
parents:
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332 my $self = shift;
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willmclaren
parents:
diff changeset
333 return $self->{'y_axis_max'} = shift if (@_);
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willmclaren
parents:
diff changeset
334 return $self->{'y_axis_max'};
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willmclaren
parents:
diff changeset
335 }
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willmclaren
parents:
diff changeset
336
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willmclaren
parents:
diff changeset
337
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willmclaren
parents:
diff changeset
338 1;