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1 // The class that deals the number of alignments supporting blocks or edges
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2 #ifndef _LSONG_RSCAF_SUPPORT_HEADER
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3 #define _LSONG_RSCAF_SUPPORT_HEADER
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4
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5 extern int minimumSupport ;
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6
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7 class Support
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8 {
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9 private:
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10 int uniqSupport ;
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11 int multiSupport ;
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12
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13 int plusSupport ;
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14 int minusSupport ;
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15
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16 int clipSupport ;
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17 int nmSum ;
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18 double multiSupportCoefficient ;
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19
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20 int64_t leftPos, rightPos ;
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21 int coordCnt ; // Record how many coordinates showed up.
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22 int64_t prevCoord ;
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23 public:
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24 Support()
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25 {
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26 uniqSupport = multiSupport = 0 ;
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27 plusSupport = minusSupport = 0 ;
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28 leftPos = rightPos = -1 ;
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29 multiSupportCoefficient = 1.0 ;
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30 nmSum = 0 ;
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31 coordCnt = 0 ;
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32 prevCoord = -1 ;
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33 }
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34
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35 ~Support()
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36 {
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37 }
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38
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39 void Add( Alignments &align, bool ignoreCoord = false )
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40 {
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41 if ( align.IsUnique() )
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42 ++uniqSupport ;
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43 else
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44 ++multiSupport ;
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45
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46 int strand = align.GetStrand() ;
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47 if ( strand == 1 )
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48 ++plusSupport ;
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49 else if ( strand == -1 )
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50 ++minusSupport ;
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51 int nm = align.GetFieldI( "NM" ) ;
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52 if ( nm >= 0 )
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53 nmSum += nm ;
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54
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55 if ( !ignoreCoord )
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56 {
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57 if ( leftPos == -1 || align.segments[0].a < leftPos )
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58 leftPos = align.segments[0].a ;
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59 if ( align.segments[ align.segCnt - 1 ].b > rightPos )
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60 rightPos = align.segments[ align.segCnt - 1 ].b ;
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61
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62 if ( align.segments[0].a != prevCoord ) // This makes sense when the coordinates are sorted
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63 ++coordCnt ;
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64 else if ( align.GetFieldZ( "SA" ) != NULL )
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65 ++coordCnt ;
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66 prevCoord = align.segments[0].a ;
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67 }
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68 }
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69
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70 void Add( Support &in )
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71 {
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72 uniqSupport += in.uniqSupport ;
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73 multiSupport += in.multiSupport ;
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74
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75 plusSupport += in.plusSupport ;
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76 minusSupport += in.minusSupport ;
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77
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78 nmSum += in.nmSum ;
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79
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80 if ( in.leftPos != -1 && ( leftPos == -1 || in.leftPos < leftPos ) )
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81 leftPos = in.leftPos ;
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82 if ( in.rightPos > rightPos )
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83 rightPos = in.rightPos ;
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84
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85 prevCoord = prevCoord > in.prevCoord ? prevCoord : in.prevCoord ;
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86 coordCnt += in.coordCnt ;
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87 }
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88
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89 bool IsGood()
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90 {
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91 if ( uniqSupport < 0.1 * ( uniqSupport + multiSupport ) || uniqSupport == 0 )
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92 return false ;
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93 if ( nmSum / ( uniqSupport + multiSupport ) >= 2.5 )
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94 return false ;
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95 return true ;
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96 }
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97
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98 bool IsUnique()
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99 {
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100 if ( uniqSupport < 0.95 * ( uniqSupport + multiSupport ) )
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101 return false ;
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102 return true ;
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103 }
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104
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105 int GetCount()
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106 {
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107 return (int)( uniqSupport + multiSupportCoefficient * multiSupport + 1e-6) ;
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108 }
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109
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110 int GetUniqCount()
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111 {
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112 return uniqSupport ;
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113 }
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114
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115 int GetStrand()
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116 {
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117 if ( plusSupport == minusSupport )
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118 return 0 ;
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119 else if ( plusSupport > minusSupport )
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120 return 1 ;
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121 else
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122 return -1 ;
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123 }
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124
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125 int GetLeftMostPos()
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126 {
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127 return leftPos ;
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128 }
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129
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130 int GetRightMostPos()
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131 {
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132 return rightPos ;
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133 }
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134
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135 int GetCoordCnt()
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136 {
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137 return coordCnt ;
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138 }
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139
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140 void operator=( const Support &in )
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141 {
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142 uniqSupport = in.uniqSupport ;
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143 multiSupport = in.multiSupport ;
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144
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145 plusSupport = in.plusSupport ;
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146 minusSupport = in.minusSupport ;
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147
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148 nmSum = in.nmSum ;
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149
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150 leftPos = in.leftPos ;
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151 rightPos = in.rightPos ;
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152
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153 multiSupportCoefficient = in.multiSupportCoefficient ;
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154
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155 prevCoord = in.prevCoord ;
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156 coordCnt = in.coordCnt ;
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157 }
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158
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159 void Clear()
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160 {
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161 uniqSupport = multiSupport = 0 ;
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162 plusSupport = minusSupport = 0 ;
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163 nmSum = 0 ;
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164 leftPos = rightPos = -1 ;
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165 multiSupportCoefficient = 1.0 ;
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166
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167 coordCnt = 0 ;
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168 prevCoord = -1 ;
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169 }
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170 } ;
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171 #endif
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