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1 #!/usr/bin/perl
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2 use strict;
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3 use warnings;
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4
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5 my $read1 = $ARGV[0];
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6 my $read2 = $ARGV[1];
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7
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8 my $output1 = $ARGV[2];
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9 my $output2 = $ARGV[3];
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10
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11 my $TYPE = $ARGV[4];
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12 my $MIN_LENGTH = $ARGV[5];
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13 my $MIN_QUALITY = $ARGV[6];
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14
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15 my $VERBOSE = $ARGV[7];
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16
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17 if (!$VERBOSE){
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18 $VERBOSE ="OFF";
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19 }
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20
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21 open(READ1, $read1) or die ("Can't open $read1\n");
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22 open(READ2, $read2) or die ("Can't open $read2\n");
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23 open(OUT1, ">$output1") or die ("Can't open $output1\n");
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24 open(OUT2, ">$output2") or die ("Can't open $output2\n");
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25
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26
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27 my $error1=0;
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28 my $error2=0;
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29 my $error3=0;
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30 my $error4=0;
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31 my $error5=0;
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32 my $error6=0;
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33 my $error7=0;
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34 my $error8=0;
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35 my $error9=0;
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36 my $error10=0;
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37
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38 while (my $ligne1_r1 =<READ1>){
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39 my $ligne2_r1 =<READ1>;
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40 my $ligne3_r1 =<READ1>;
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41 my $ligne4_r1 =<READ1>;
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42 my $ligne1_r2 =<READ2>;
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43 my $ligne2_r2 =<READ2>;
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44 my $ligne3_r2 =<READ2>;
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45 my $ligne4_r2 =<READ2>;
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46
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47 #@ 1 sec
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48 if ((!$ligne1_r1)||(!$ligne2_r1)||(!$ligne3_r1)||(!$ligne4_r1)||(!$ligne1_r2)||(!$ligne2_r2)||(!$ligne3_r2)||(!$ligne4_r2)){
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49 if ($VERBOSE eq "ON"){
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50 print "Error in file format";
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51 if ($ligne1_r1){print $ligne1_r1;}
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52 if ($ligne2_r1){print $ligne2_r1;}
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53 if ($ligne3_r1){print $ligne3_r1;}
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54 if ($ligne4_r1){print $ligne4_r1;}
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55 if ($ligne1_r2){print $ligne1_r2;}
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56 if ($ligne2_r2){print $ligne2_r2;}
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57 if ($ligne3_r2){print $ligne3_r2;}
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58 if ($ligne4_r2){print $ligne4_r2;}
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59 print "\n";
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60 }
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61 $error1++;
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62 }
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63 elsif(($ligne1_r1 !~/^\@/)||($ligne1_r2 !~/^\@/)||($ligne3_r1 !~/^\+/)||($ligne3_r2 !~/^\+/)){
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64 if ($VERBOSE eq "ON"){
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65 print "Error in header : format\n";
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66 print $ligne1_r1;
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67 print $ligne2_r1;
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68 print $ligne3_r1;
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69 print $ligne4_r1;
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70 print $ligne1_r2;
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71 print $ligne2_r2;
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72 print $ligne3_r2;
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73 print $ligne4_r2;
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74 print "\n";
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75 }
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76 $error2++;
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77 }
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78 #@ 1 - 2 sec
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79 else {
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80
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81 my $length_seq1 = length($ligne2_r1);
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82 my $length_qual1 =length($ligne4_r1);
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83 my $seq1;
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84 my $qual1;
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85
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86 my $length_seq2 = length($ligne2_r2);
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87 my $length_qual2 =length($ligne4_r2);
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88 my $seq2;
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89 my $qual2;
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90 my $header1="";
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91 my $header2="";
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92 my $repheader1="";
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93 my $repheader2="";
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94
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95 if ($ligne1_r1 =~/^\@(.*?)\#/){
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96 $header1 = $1;
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97 }
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98
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99 if ($ligne3_r1 =~/^\+(.*?)\#/){
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100 $repheader1 = $1;
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101 }
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102
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103 if ($ligne1_r2 =~/^\@(.*?)\#/){
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104 $header2 = $1;
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105 }
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106
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107 if ($ligne3_r2 =~/^\+(.*?)\#/){
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108 $repheader2 = $1;
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109 }
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110 #@ 2 sec
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111
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112 ### Verification de la coherence sequence /qualité @ 1 sec
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113 if (($TYPE eq "illumina")&&((!$header1)||(!$header2)||(!$repheader1)||(!$repheader2))){
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114 if ($VERBOSE eq "ON"){
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115 print "Error in header : empty\n";
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116 print $ligne1_r1;
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117 print $ligne2_r1;
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118 print $ligne3_r1;
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119 print $ligne4_r1;
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120 print $ligne1_r2;
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121 print $ligne2_r2;
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122 print $ligne3_r2;
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123 print $ligne4_r2;
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124 print "\n";
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125 }
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126 $error3++;
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127 }
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128 elsif (($TYPE eq "sanger")&&((!$header1)||(!$header2))){
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129 if ($VERBOSE eq "ON"){
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130 print "Error in header refgsd : empty\n";
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131 print $ligne1_r1;
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132 print $ligne2_r1;
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133 print $ligne3_r1;
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134 print $ligne4_r1;
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135 print $ligne1_r2;
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136 print $ligne2_r2;
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137 print $ligne3_r2;
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138 print $ligne4_r2;
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139 print "\n";
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140 }
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141 $error3++;
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142 }
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143 elsif (($TYPE eq "illumina")&&(($header1 ne $repheader1)||($header2 ne $repheader2)||($header1 ne $header2))){
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144 if ($VERBOSE eq "ON"){
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145 print "Error in header : different\n";
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146 print $ligne1_r1;
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147 print $ligne2_r1;
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148 print $ligne3_r1;
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149 print $ligne4_r1;
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150 print $ligne1_r2;
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151 print $ligne2_r2;
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152 print $ligne3_r2;
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153 print $ligne4_r2;
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154 print "\n";
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155 }
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156 $error4++;
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157 }
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158 elsif (($TYPE eq "sanger")&&($header1 ne $header2)){
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159 if ($VERBOSE eq "ON"){
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160 print "Error in header : different\n";
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161 print $ligne1_r1;
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162 print $ligne2_r1;
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163 print $ligne3_r1;
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164 print $ligne4_r1;
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165 print $ligne1_r2;
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166 print $ligne2_r2;
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167 print $ligne3_r2;
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168 print $ligne4_r2;
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169 print "\n";
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170 }
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171 $error4++;
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172 }
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173 elsif (($length_seq1 != $length_qual1)||($length_seq2 != $length_qual2)){
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174 if ($VERBOSE eq "ON"){
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175 print "Error in seq/qual length\n";
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176 print $ligne1_r1;
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177 print $ligne2_r1;
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178 print $ligne3_r1;
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179 print $ligne4_r1;
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180 print $ligne1_r2;
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181 print $ligne2_r2;
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182 print $ligne3_r2;
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183 print $ligne4_r2;
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184 print "\n";
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185 }
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186 $error5++;
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187 }
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188 #@ 1 - 2 sec
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189 else {
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190 ### Parsing sequence & qualité
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191 if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){
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192 $seq1 = $1;
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193 }
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194 if ($ligne2_r2 =~ /^([ATGCNX]+)\s*$/i){
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195 $seq2 = $1;
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196 }
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197 if ($ligne4_r1 =~ /^(.*)\s*$/i){
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198 $qual1 = $1;
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199 }
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200 if ($ligne4_r2 =~ /^(.*)\s*$/i){
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201 $qual2 = $1;
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202 }
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203 #@ 2 sec
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204 ### Verification du parsing et de la coherence sequence /qualité (n°2)
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205 if ((!$seq1)||(!$seq2)||(!$qual1)||(!$qual2)){
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206 if ($VERBOSE eq "ON"){
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207 print "Error parsing seq / quality \n";
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208 print $ligne1_r1;
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209 print $ligne2_r1;
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210 print $ligne3_r1;
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211 print $ligne4_r1;
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212 print $ligne1_r2;
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213 print $ligne2_r2;
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214 print $ligne3_r2;
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215 print $ligne4_r2;
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216 print "\n";
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217 }
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218 $error6++;
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219 }
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220 elsif ((length($seq1) != length($qual1))||(length($seq2) != length($qual2))){
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221 if ($VERBOSE eq "ON"){
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222 print "Error in seq/qual length after parsing\n";
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223 print $ligne1_r1;
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224 print $ligne2_r1;
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225 print $ligne3_r1;
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226 print $ligne4_r1;
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227 print $ligne1_r2;
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228 print $ligne2_r2;
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229 print $ligne3_r2;
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230 print $ligne4_r2;
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231 print "\n";
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232 }
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233 $error7++;
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234 }
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235 #@ <1 sec
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236 else {
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237 my $fastq_lines_r1="";
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238 my $fastq_lines_r2="";
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239 $fastq_lines_r1 = &grooming_and_trimming($ligne1_r1,$seq1,$qual1);
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240 if ($fastq_lines_r1){
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241 $fastq_lines_r2 = &grooming_and_trimming($ligne1_r2,$seq2,$qual2);
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242 }
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243 if ($fastq_lines_r2){
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244 print OUT1 $fastq_lines_r1;
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245 print OUT2 $fastq_lines_r2;
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246 }
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247 }
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248 }
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249
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250 # print OUT1 $ligne1_r1;
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251 # print OUT1 $ligne2_r1;
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252 # print OUT1 $ligne3_r1;
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253 # print OUT1 $ligne4_r1;
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254 # print OUT2 $ligne1_r2;
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255 # print OUT2 $ligne2_r2;
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256 # print OUT2 $ligne3_r2;
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257 # print OUT2 $ligne4_r2;
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258
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259 #@ 7 sec
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260 }
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261 }
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262
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263
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264
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265 close (READ1);
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266 close (READ2);
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267 close (OUT1);
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268 close (OUT2);
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269
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270
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271
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272
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273 sub grooming_and_trimming{
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274 my $header = shift;
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275 my $seq = shift;
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276 my $quality = shift;
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277 my $quality_converted="";
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278
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279 my $startnoN = 0;
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280 my $stopnoN = length($quality)-1;
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281
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4
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282 #print "HEAD:\t$header";
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283 #print "SEQ:\t$seq\n";
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0
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284
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285 my $chercheN = $seq;
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286 my @bad_position;
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287 my $current_index = index($chercheN,"N");
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288 my $abs_index = $current_index;
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289 while ($current_index >=0){
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290 push (@bad_position,$abs_index);
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291
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292 if ($current_index<length($seq)){
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293 $chercheN = substr($chercheN,$current_index+1);
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294 $current_index = index($chercheN,"N");
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295 $abs_index = $current_index + $bad_position[$#bad_position]+1;
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296 }
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297 else {
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298 last;
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299 }
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300 }
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301
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302
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303 if ($#bad_position>=0){
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304 my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)};
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305 $startnoN = $coord{"start"};
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306 $stopnoN = $coord{"stop"};
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307 }
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308 my $lengthnoN = $stopnoN - $startnoN + 1;
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309 my $seqnoN = substr($seq,$startnoN,$lengthnoN);
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4
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310 # print "SEQnoN\t:$seqnoN\n";
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311 # for (my $i=0;$i<=$#bad_position;$i++){
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312 # print $bad_position[$i]."\t";
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313 # }
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314 # print "\n";
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0
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315
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316 if ($lengthnoN >= $MIN_LENGTH){
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317 my $startTrim = $startnoN;
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318 my $stopTrim = $stopnoN;
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319
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320 my $quality_converted="";
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4
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321 #my @bad_position;
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0
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322
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323 my @q = split(//,$quality);
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324 #print "QUALITY\n";
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325 #print "$quality\n";
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326 for (my $i=0;$i<=$stopnoN;$i++){
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327 my $chr = $q[$i];
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328 my $num = ord($q[$i]);
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329 if ($TYPE eq "illumina"){
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330 $num = $num -64+33;
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331 $quality_converted .= chr($num);
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332 }
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333
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334 if ($num <$MIN_QUALITY + 64 - 33 ){
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335 push(@bad_position,$i+$startnoN);
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336 }
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337 }
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338 if ($quality_converted){$quality = $quality_converted;}
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339 #print "$quality\n";
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340
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341
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342
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343 if ($#bad_position>=0){
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4
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344 @bad_position = sort {$a <=> $b} @bad_position;
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345 # for (my $i=0;$i<=$#bad_position;$i++){
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346 # print $bad_position[$i]."\t";
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347 # }
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348 # print "\n";
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0
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349 my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)};
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350 $startTrim = $coord{"start"};
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351 $stopTrim = $coord{"stop"};
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352 #print "$startTrim .. $stopTrim\n";
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353
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354 }
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355 my $lengthTrim = $stopTrim - $startTrim +1;
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356
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357
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358 my $fastq_lines="";
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359
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360 if ($lengthTrim >= $MIN_LENGTH){
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361 $fastq_lines .= $header;
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362 $fastq_lines .= substr($seq,$startTrim,$lengthTrim)."\n";
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363 $fastq_lines .= "+\n";
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364 $fastq_lines .= substr($quality,$startTrim,$lengthTrim)."\n";
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4
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365 # print $fastq_lines;
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0
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366 return $fastq_lines;
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4
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367
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0
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368 }
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369 else {
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370 return "";
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371 }
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372
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373
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374
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375 }
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376 else {
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377 return "";
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378 }
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379
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380
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381 # my @s = split(//,$seq);
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382 # my $sanger_quality="";
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383
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384
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385
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386
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387 # return $sanger_quality;
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388 }
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389
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390 sub extract_longer_string_coordinates_from_bad_position{
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391 my $start=shift;
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392 my $stop =shift;
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393 my $refbad = shift;
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394 my @bad_position = @$refbad;
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395 my %coord;
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396
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397 my $current_start = $start;
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398 my $current_stop = $bad_position[0]-1;
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399 if ($current_stop < $start){$current_stop = $start;}
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400
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401
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402 #debut -> premier N
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403 my $current_length = $current_stop - $current_start +1;
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404 my $test_length;
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405
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406 #entre les N
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407 for (my $i=1;$i<=$#bad_position;$i++){
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408 $test_length = $bad_position[$i]+1-$bad_position[$i-1]-1;
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409 if ( $test_length > $current_length){
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410 $current_start = $bad_position[$i-1]+1;
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411 $current_stop = $bad_position[$i]-1;
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412 $current_length = $current_stop - $current_start +1;
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413 }
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414 }
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415
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416 #dernier N -> fin
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417 $test_length = $stop-$bad_position[$#bad_position]+1;
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418 if ( $test_length > $current_length){
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419 $current_start = $bad_position[$#bad_position]+1;
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420 if ($current_start > $stop){$current_start=$stop;}
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421 $current_stop = $stop;
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422 }
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423 $coord{"start"}=$current_start;
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424 $coord{"stop"}= $current_stop;
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425 $coord{"lenght"}=$current_stop-$current_start+1;
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426
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427 return \%coord;
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428 }
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