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0
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1
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2 mkdir -p tmp
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3
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15
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4 echo "# Test codonlogo by building logos with many different options."
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5
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6 echo -ne '.'
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15
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7 ./codonlogo < cap.fa > tmp/logo0.eps ||exit
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8
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9 echo -ne '.'
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15
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10 ./codonlogo --title "Default Logo with Title" < cap.fa > tmp/logo1.eps ||exit
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0
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11
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12 echo -ne '.'
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15
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13 ./codonlogo --debug yes --fineprint "Default Logo with this fineprint and debug on" < cap.fa > tmp/logo2.eps ||exit
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0
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14
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15 echo -ne '.'
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15
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16 ./codonlogo --debug no --fineprint "--debug no" --debug no < cap.fa > tmp/logo3.eps ||exit
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0
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17
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18 echo -ne '.'
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15
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19 ./codonlogo --debug yes --fineprint "" --title "No fine print" --debug yes < cap.fa > tmp/logo4.eps ||exit
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20
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21 echo -ne '.'
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15
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22 ./codonlogo --debug yes --fineprint "No title" --title "" < cap.fa > tmp/logo5.eps ||exit
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23
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24 echo -ne '.'
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15
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25 ./codonlogo --debug yes --fineprint "--first-index -10" --first-index -10 < cap.fa > tmp/logo6.eps ||exit
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26
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27 echo -ne '.'
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28 ./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 11 " --first-index -10 --stacks-per-line 11 < cap.fa > tmp/logo7a.eps ||exit
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29
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30 echo -ne '.'
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15
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31 ./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 8 " --first-index -10 --stacks-per-line 8 < cap.fa > tmp/logo7b.eps ||exit
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0
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32
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33 echo -ne '.'
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15
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34 ./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 7 " --first-index -10 --stacks-per-line 7 < cap.fa > tmp/logo7c.eps ||exit
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0
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35
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36 echo -ne '.'
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15
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37 ./codonlogo --debug yes --fineprint "Test fin and fout" --fin cap.fa --fout logo8.eps ||exit
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38
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39 # Test Y Axis
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40
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41 echo -ne '.'
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15
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42 ./codonlogo --debug yes --fineprint "Custom yaxis label " --ylabel 'yaxis label' < cap.fa > tmp/logo9a.eps ||exit
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0
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43
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44 echo -ne '.'
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15
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45 ./codonlogo --debug yes --fineprint "Custom units" --units 'nats' < cap.fa > tmp/logo9b.eps ||exit
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0
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46
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47 echo -ne '.'
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15
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48 ./codonlogo --debug yes --fineprint "Override custom units with custom yaxis label." --ylabel 'yaxis label' --units nats < cap.fa > tmp/logo9c.eps ||exit
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0
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49
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50 echo -ne '.'
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15
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51 ./codonlogo --debug yes --fineprint "Empty ylabel" --ylabel '' < cap.fa > tmp/logo9d.eps
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0
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52
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53 echo -ne '.'
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15
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54 ./codonlogo --debug yes --fineprint "No Yaxis" --show-yaxis no < cap.fa > tmp/logo9e.eps ||exit
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0
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55
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56 # Test X Axis
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57
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58 echo -ne '.'
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15
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59 ./codonlogo --debug yes --format pdf --fineprint "Custom xaxis label " --xlabel 'xaxis label' < cap.fa > tmp/logo10a.pdf ||exit
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0
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60
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61 echo -ne '.'
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15
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62 ./codonlogo --debug yes --format pdf --fineprint "Empty xlabel" --xlabel '' < cap.fa > tmp/logo10b.pdf ||exit
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0
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63
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64 echo -ne '.'
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15
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65 ./codonlogo --debug yes --format pdf --fineprint "No Xaxis" --show-xaxis no < cap.fa > tmp/logo10c.pdf ||exit
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0
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66
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67 echo -ne '.'
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15
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68 ./codonlogo --debug yes --format pdf --fineprint "No Xaxis, custom label" --xlabel "Custom xlabel" --show-xaxis no < cap.fa > tmp/logo10d.pdf ||exit
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0
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69
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70 # Test Formats
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71
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72 echo -ne '.'
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15
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73 ./codonlogo --debug no --fineprint "Format: eps" --format eps < cap.fa > tmp/logo11a.eps ||exit
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0
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74
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75 echo -ne '.'
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15
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76 ./codonlogo --debug no --fineprint "Format: png" --size large --format png < cap.fa > tmp/logo11b.png ||exit
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0
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77
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78 echo -ne '.'
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15
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79 ./codonlogo --debug no --fineprint "Format: png high res" --format png_print < cap.fa > tmp/logo11c.png ||exit
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0
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80
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81 echo -ne '.'
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15
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82 ./codonlogo --debug no --fineprint "Format: pdf" --format pdf < cap.fa > tmp/logo11d.pdf ||exit
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0
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83
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84 echo -ne '.'
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15
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85 ./codonlogo --debug no --fineprint "Format: jpeg" --size large --format jpeg < cap.fa > tmp/logo11e.jpeg ||exit
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0
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86
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87 echo -ne '.'
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15
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88 ./codonlogo --debug no --fineprint "Format: EPS" --format EPS < cap.fa > tmp/logo11f.eps ||exit
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0
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89
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90 # Test Sizes
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91
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92 echo -ne '.'
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15
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93 ./codonlogo --debug no --format png_print --fineprint "default size" < cap.fa > tmp/logo12_default.png ||exit
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0
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94
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95 echo -ne '.'
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15
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96 ./codonlogo --debug no --format png_print --fineprint "--size large" --size large < cap.fa > tmp/logo12_large.png ||exit
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0
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97
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98 echo -ne '.'
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15
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99 ./codonlogo --debug no --format png_print --fineprint "--size medium" --size medium < cap.fa > tmp/logo12_medium.png ||exit
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0
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100
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101 echo -ne '.'
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15
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102 ./codonlogo --debug no --format png_print --fineprint "--size small" --size small < cap.fa > tmp/logo12_small.png ||exit
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0
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103
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104
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105
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106 echo -ne '.'
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15
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107 ./codonlogo --format pdf --fineprint "" > tmp/logo13.pdf << LimitString
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0
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108 >
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109 GTTGTTGTTGTT
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110 >
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111 GTCGTCGTCGTC
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112 >
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113 GGGGGGGGGGGG
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114 >
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115 GGAGGAGGAGGA
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116 LimitString
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117
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118
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119
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120
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121 # Test unit options
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122 echo -ne '.'
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15
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123 ./codonlogo --format pdf --fineprint "probability" --unit probability > tmp/logo14a.pdf < cap.fa ||exit
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0
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124
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125
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126
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127
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128
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129
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130
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15
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131
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