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annotate duplex.sublime-workspace @ 4:af383638de66 draft

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planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
author nick
date Mon, 23 Nov 2015 18:44:23 -0500
parents
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4
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1 {
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2 "auto_complete":
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3 {
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4 "selected_items":
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5 [
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6 [
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7 "can",
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8 "can_change_color function"
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9 ],
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10 [
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11 "NAI",
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12 "NAIVE_TEST_THRES"
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13 ],
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14 [
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15 "curre",
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16 "current_seq statement"
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17 ],
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18 [
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19 "align",
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20 "align_path statement"
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21 ],
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22 [
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23 "Att",
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24 "AttributeError class"
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25 ],
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26 [
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27 "pipe",
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28 "pipeline_family_choose_asm function"
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29 ],
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30 [
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31 "Obj",
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32 "ObjectsById"
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33 ],
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34 [
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35 "get",
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36 "getElementById"
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37 ],
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38 [
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39 "make",
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40 "makeStatElem"
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41 ],
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42 [
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43 "timeTo",
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44 "timeToNextReindeer"
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45 ],
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46 [
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47 "golden",
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48 "goldenUpgrades"
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49 ],
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50 [
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51 "How",
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52 "HowMuchPrestige"
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53 ],
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54 [
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55 "HTTP",
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56 "HTTPLIB_PARAMS statement"
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57 ],
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58 [
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59 "ISNV",
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60 "ISNVFILE_DEFAULT statement"
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61 ],
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62 [
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63 "DA",
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64 "DATA_DIR_DEFAULT statement"
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65 ],
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66 [
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67 "REQ",
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68 "REQUIRED_PICARDS statement"
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69 ],
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70 [
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71 "add_ar",
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72 "add_argument_group function"
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73 ],
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74 [
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75 "sample_fam",
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76 "sample_family_rows statement"
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77 ],
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78 [
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79 "SAM",
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80 "SAMPLES_FILE statement"
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81 ],
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82 [
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83 "spi",
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84 "spikein_str statement"
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85 ],
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86 [
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87 "scri",
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88 "scriptdir"
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89 ],
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90 [
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91 "IGNO",
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92 "IGNORE_EXTS statement"
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93 ],
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94 [
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95 "watch",
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96 "watch_progs"
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97 ],
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98 [
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99 "IG",
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100 "IGNORE_EXTS statement"
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101 ],
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102 [
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103 "Dev",
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104 "DeviceDefault"
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105 ],
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106 [
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107 "cac",
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108 "cache_file"
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109 ],
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110 [
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111 "Asn",
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112 "AsnMacCache"
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113 ],
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114 [
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115 "gate",
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116 "gateway_ip"
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117 ],
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118 [
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119 "getE",
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120 "getElementsByClassName"
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121 ],
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122 [
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123 "high",
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124 "highlightTerms"
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125 ],
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126 [
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127 "medi",
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128 "mediaElement"
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129 ],
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130 [
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131 "get_mp",
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132 "get_mp3_name"
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133 ],
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134 [
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135 "pl",
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136 "player_url"
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137 ],
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138 [
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139 "fa",
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140 "fastq1"
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141 ],
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142 [
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143 "ba",
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144 "backgrounded"
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145 ],
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146 [
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147 "human",
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148 "human_time statement"
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149 ],
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150 [
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151 "NotI",
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152 "NotImplementedError class"
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153 ],
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154 [
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155 "recu",
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156 "recursively"
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158 [
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159 "SAMPLES",
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160 "SAMPLES_HEADER statement"
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161 ],
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162 [
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163 "wildcard",
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164 "wildcard_match function"
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165 ],
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166 [
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167 "existing",
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168 "existing_samples statement"
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169 ],
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170 [
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171 "SAPL",
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172 "SAMPLES_HEADER statement"
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173 ],
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174 [
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175 "max",
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176 "max_tz_diff"
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177 ],
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178 [
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179 "bio",
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180 "bio_sample_id statement"
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181 ],
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182 [
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183 "tech",
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184 "technology"
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185 ],
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186 [
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187 "HEA",
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188 "HEADER_JOINED statement"
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189 ],
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190 [
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191 "Z_B",
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192 "Z_BORDER"
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193 ],
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194 [
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195 "BA",
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196 "BASE_SIZE"
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197 ],
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198 [
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199 "destroy",
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200 "destroyRecursive"
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201 ],
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202 [
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203 "sam",
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204 "sample_regex"
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205 ],
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206 [
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207 "pair",
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208 "pair_regex"
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209 ],
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210 [
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211 "edge",
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212 "edge_effect"
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213 ],
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214 [
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215 "XRA",
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216 "XRANDR_DISP_REGEX"
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217 ],
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218 [
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219 "eh",
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220 "exho"
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221 ],
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222 [
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223 "MIN",
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224 "MINUS2_SRC"
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225 ],
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226 [
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227 "filename",
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228 "filename_new"
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229 ],
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230 [
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231 "MUL",
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232 "MULTI_REPLACE"
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233 ],
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234 [
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235 "IMG",
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236 "REGEX_IMGUR_SRC"
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237 ],
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238 [
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239 "lan_",
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240 "lan_ip_current"
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241 ],
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242 [
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243 "BUFF",
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244 "BUFFER_MAX"
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245 ],
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246 [
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247 "passed",
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248 "passed_filters"
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249 ],
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250 [
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251 "getCo",
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252 "getCoverageGap"
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253 ],
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254 [
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255 "GAME_",
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256 "GAME_WIDTH"
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257 ],
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258 [
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259 "GAME",
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260 "GAME_WIDTH"
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261 ],
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262 [
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263 "visi",
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264 "visibility"
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265 ],
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266 [
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267 "source",
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268 "source_file"
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269 ],
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270 [
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271 "like",
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272 "likeliest_count"
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273 ],
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274 [
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275 "cso",
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276 "csource_path_fixed"
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277 ],
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278 [
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279 "csou",
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280 "csource_path"
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281 ],
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282 [
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283 "csour",
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284 "csource_file"
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287 "buffe",
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335 "FAS",
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336 "FASTA_WIDTH"
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339 "new",
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340 "new_chrom"
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343 "rig",
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344 "right_block"
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347 "USE",
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348 "USER_AGENT_BROWSER"
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351 "query",
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352 "query_interval"
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355 "next",
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356 "next_interval"
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359 "final",
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360 "final_sequence"
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363 "subje",
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364 "subject_name"
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366 [
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367 "summary",
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368 "summary_fxn"
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371 "summ",
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372 "summary_fxn"
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375 "D",
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376 "DISTRIB_ID"
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379 "DEF",
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380 "DEFAULT_SIZE"
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383 "state",
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384 "state_filepath"
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387 "data",
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388 "data_filepath"
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391 "des",
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392 "desktop_size"
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395 "matpl",
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399 "fig",
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403 "search",
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407 },
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408 "buffers":
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411 "file": "/home/me/bx/project/ebola/compare/vcf-vs-tsv.py",
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412 "settings":
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414 "buffer_size": 5574,
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415 "line_ending": "Unix"
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416 }
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417 },
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419 "file": "sscs.py",
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420 "settings":
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422 "buffer_size": 11029,
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423 "line_ending": "Unix"
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424 }
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425 },
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427 "file": "stats.py",
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428 "settings":
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429 {
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430 "buffer_size": 3713,
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431 "line_ending": "Unix"
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432 }
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433 },
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434 {
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435 "file": "/home/me/bx/code/duplex/align.c",
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436 "settings":
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437 {
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438 "buffer_size": 7383,
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439 "line_ending": "Unix"
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440 }
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441 },
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442 {
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443 "file": "pipeline.sh",
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444 "settings":
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445 {
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446 "buffer_size": 2314,
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447 "line_ending": "Unix"
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448 }
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449 }
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450 ],
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451 "build_system": "",
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452 "build_system_choices":
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453 [
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454 ],
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455 "build_varint": "",
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456 "command_palette":
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457 {
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458 "height": 392.0,
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459 "last_filter": "",
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460 "selected_items":
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461 [
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462 [
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463 "folder",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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464 "Project: Add Folder"
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465 ],
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466 [
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467 "ana",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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468 "Anaconda: Next lint error"
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469 ],
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470 [
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471 "js",
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472 "JSHint"
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473 ],
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474 [
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475 "install package",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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476 "Package Control: Install Package"
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477 ],
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478 [
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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479 "disp",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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480 "Anaconda: Display object docs"
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481 ],
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482 [
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483 "goto",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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484 "Anaconda: Goto object definition"
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485 ],
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486 [
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487 "",
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488 "Anaconda: McCabe complexity check"
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489 ],
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490 [
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491 "package",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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492 "Package Control: Install Package"
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493 ],
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494 [
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495 "jshint",
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496 "JSHint: Set Linting Preferences"
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497 ]
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498 ],
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499 "width": 530.0
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500 },
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501 "console":
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502 {
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503 "height": 126.0,
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504 "history":
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505 [
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506 "import urllib.request,os,hashlib; h = '7183a2d3e96f11eeadd761d777e62404' + 'e330c659d4bb41d3bdf022e94cab3cd0'; pf = 'Package Control.sublime-package'; ipp = sublime.installed_packages_path(); urllib.request.install_opener( urllib.request.build_opener( urllib.request.ProxyHandler()) ); by = urllib.request.urlopen( 'http://sublime.wbond.net/' + pf.replace(' ', '%20')).read(); dh = hashlib.sha256(by).hexdigest(); print('Error validating download (got %s instead of %s), please try manual install' % (dh, h)) if dh != h else open(os.path.join( ipp, pf), 'wb' ).write(by)",
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507 "sublime",
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508 "print 1",
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509 "type(None)",
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510 "print None",
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511 "None",
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512 "a*3",
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513 "if a:",
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514 "if a: print \"a\"",
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515 "a = 2",
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516 "1",
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517 "echo 1",
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518 "print 1",
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
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519 "1"
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520 ]
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521 },
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522 "distraction_free":
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523 {
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524 "menu_visible": true,
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525 "show_minimap": false,
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526 "show_open_files": false,
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527 "show_tabs": false,
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528 "side_bar_visible": false,
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529 "status_bar_visible": false
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530 },
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531 "expanded_folders":
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532 [
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533 "/home/me/bx/code/duplex"
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534 ],
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535 "file_history":
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536 [
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537 "/home/me/code/test.sublime-project",
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538 "/home/me/annex/Work/PSU/Nekrutenko/code/indels/dev/group-filter.py",
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539 "/home/me/bx/code/indels/dev/pipeline.py",
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540 "/home/me/annex/Work/PSU/Nekrutenko/code/indels/dev/pipeline-families.sh",
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541 "/home/me/annex/Work/PSU/Nekrutenko/code/heteroplasmy/pipeline-summary.sh",
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542 "/home/me/annex/Work/PSU/Nekrutenko/code/indels/dev/pipeline-family.py",
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543 "/home/me/annex/Work/PSU/Nekrutenko/code/heteroplasmy/pipeline-nvc-cvg.sh",
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544 "/home/me/annex/Work/PSU/Nekrutenko/code/heteroplasmy/pipeline.sh",
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545 "/home/me/annex/Work/PSU/Nekrutenko/code/duplex/tests/run.sh",
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546 "/home/me/annex/Work/PSU/Nekrutenko/code/duplex/align.py",
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547 "/home/me/code/python/wifi/wifi-login.py",
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548 "/home/me/annex/Work/PSU/Nekrutenko/src/scalpel-0.3.2/bcftools-1.1/vcffilter.c",
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549 "/home/me/annex/Saved Web Stuff/Webpages/7 bonerparty/2008-10-02/bonerparty-page-8-2008-10-03.html",
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550 "/home/me/annex/Work/PSU/Nekrutenko/code/indels/dev/get-indels.py",
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551 "/home/me/annex/Work/PSU/Nekrutenko/berkeley/pruning/bases.c",
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552 "/home/me/code/c/test/linked.c",
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553 "/home/me/bx/code/duplex/sscs.py",
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554 "/home/me/code/bash/dotfiles/.bashrc",
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555 "/home/me/bx/code/heteroplasmy/power.R",
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658 "/home/me/annex/Work/PSU/Nekrutenko/code/allele_counts/shedvps/allele-counts.xml",
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660 "/home/me/annex/Work/PSU/Nekrutenko/code/indels/dev/inspect-reads.py",
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661 "/home/me/backuphide/bfx/galaxy-central/eggs/Fabric-1.7.0-py2.7.egg/fabric/contrib/console.py",
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663 "/home/me/annex/Work/PSU/Nekrutenko/code/indels/dev/asm-curator.py",
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664 "/home/me/aa/misc/travel/Google Maps maps/State College.kml"
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665 ],
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666 "find":
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667 {
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668 "height": 35.0
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669 },
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670 "find_in_files":
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671 {
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672 "height": 0.0,
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673 "where_history":
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674 [
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675 ]
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676 },
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677 "find_state":
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678 {
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679 "case_sensitive": false,
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680 "find_history":
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681 [
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682 "int",
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683 "int_array_pointer",
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684 "int_array_p",
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685 "10",
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686 "stat",
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687 "VALUE",
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688 "barcode",
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689 "half",
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690 "tr",
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691 "AwkScript",
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692 "get_diffs_simple",
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693 "in_gap",
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694 "output",
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695 "2",
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696 "get_diffs_binned",
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697 "2",
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698 "get_diffs",
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699 "family, consensus",
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700 "get_all_diffs",
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701 "family_barcode",
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702 "barcode",
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703 "family_barcode",
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704 "stats_file",
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705 "open_workers",
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706 "NamedTemporaryFile",
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707 "delete_tempfiles",
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708 " \"$",
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709 "process_family",
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710 "all_families",
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711 "process_family",
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712 "total_",
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713 "total_time",
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714 "process_family",
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715 "pecol",
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716 "git",
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717 "black",
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718 "dead",
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719 "window",
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720 "insert_gaps",
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721 "Element",
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722 "tip",
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723 "make_tree",
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724 "Node",
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725 "node",
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726 "Node",
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727 "i",
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728 "new_i",
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729 "offset2",
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730 "offset1",
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731 "j",
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732 "i",
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733 "_fwd_match",
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734 "a",
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735 "A",
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736 "a",
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737 "N_TEST_PCT",
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738 "N_TEST_BP",
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739 "testlib",
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740 ">>>",
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741 "seqlen",
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742 "chrom",
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743 "CHROM",
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744 "chrom",
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745 "CHROM_DEFAULT",
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746 "chrM",
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747 "FASTA",
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748 "fasta",
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749 "sam",
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750 "Sam",
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751 "sam",
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752 "chrom",
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753 "CHROM",
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754 "chrom",
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755 "CHROM",
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756 "chrom",
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757 "size",
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758 "SIZE",
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759 "size",
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760 "PHRED_THRES",
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761 "allowed_flags",
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762 "ALLOWED_FLAGS",
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763 "MAPQ_THRES",
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764 "CHROM",
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765 "chrom",
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766 "DEFAULT_CHROM",
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767 "chrom",
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768 "DEFAULT_CHROM",
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769 "chrom",
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770 "DEFAULT_CHROM",
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771 "disttbfast",
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772 "mafft",
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773 "argv",
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774 "current_seq",
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775 "fastx",
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776 "em_cons",
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777 "NamedTemporaryFile",
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778 "tempfile",
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779 "open_workers",
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780 "compile_results",
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781 "open_workers",
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782 "tmp",
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783 "base",
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784 "TMP",
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785 "sscs",
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786 "write",
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787 "logging",
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788 "msa",
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789 "cons_path",
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790 "first_line",
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791 "temp_file",
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792 "tmp_path",
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793 "subprocess",
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794 "temp_file1",
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795 "tmp_path1",
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796 "current_barcode",
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797 "mark_user_deleted",
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798 "git",
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799 "mafft",
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800 "meta",
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801 "count2",
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802 "seq2_keep",
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803 "seq1_keep",
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804 "AWK_EDGE",
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805 "summarize_site",
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806 "print_site",
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807 "1000",
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808 "ns2",
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809 "ns1"
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810 ],
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811 "highlight": true,
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812 "in_selection": false,
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813 "preserve_case": false,
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814 "regex": false,
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815 "replace_history":
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816 [
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817 "NBSgoal",
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818 "pct",
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819 "args.end >",
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820 "$tmp",
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821 "\\'",
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822 "watch",
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823 "Watch",
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824 "watch",
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825 "yoga",
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826 "Game.numReads",
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827 "Game.cell",
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828 "Panels.popup",
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829 "Panels.main",
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830 "Panels.param",
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831 "Panels.bank",
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832 "Panels.main",
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833 "main",
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834 "Panels.main",
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835 "main",
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836 "Panels.main",
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837 "consensus",
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838 "Panels.consensus",
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839 "\\'",
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840 "function $1 ",
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841 "function $1",
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842 "function $1 ",
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843 "$dir/asm.fa",
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844 "param",
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845 "lastpass",
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846 "', '",
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847 ".attr({x",
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848 "MAIN",
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849 "_col",
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850 "_ct",
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851 "Regex",
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852 "google.com",
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853 "Regexen.",
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854 "'));",
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855 ".push(",
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856 "\"",
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857 "gap.end",
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858 "gap.start",
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859 "MAIN.height",
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860 "MAIN.width",
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861 "MAIN.y",
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862 "MAIN.x",
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863 " ---\"",
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864 "--- ",
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865 "intermediates ",
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866 "args['\\1']",
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867 "args."
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868 ],
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869 "reverse": false,
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870 "show_context": true,
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871 "use_buffer2": true,
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872 "whole_word": false,
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873 "wrap": true
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874 },
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875 "groups":
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876 [
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877 {
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878 "selected": 2,
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879 "sheets":
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880 [
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881 {
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882 "buffer": 0,
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883 "file": "/home/me/bx/project/ebola/compare/vcf-vs-tsv.py",
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884 "semi_transient": false,
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885 "settings":
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886 {
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887 "buffer_size": 5574,
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888 "regions":
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889 {
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890 },
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891 "selection":
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892 [
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893 [
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894 3646,
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895 3646
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896 ]
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897 ],
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898 "settings":
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899 {
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900 "syntax": "Packages/Python/Python.tmLanguage",
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901 "tab_size": 2,
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902 "translate_tabs_to_spaces": true
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903 },
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904 "translation.x": 0.0,
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905 "translation.y": 1194.0,
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906 "zoom_level": 1.0
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907 },
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908 "stack_index": 3,
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909 "type": "text"
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910 },
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911 {
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912 "buffer": 1,
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913 "file": "sscs.py",
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914 "semi_transient": false,
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915 "settings":
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916 {
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917 "buffer_size": 11029,
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918 "regions":
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919 {
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920 },
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921 "selection":
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922 [
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924 3494,
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925 3494
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926 ]
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927 ],
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928 "settings":
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929 {
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930 "syntax": "Packages/Python/Python.tmLanguage",
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1070 },
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1071 "output.find_results":
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1072 {
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1073 "height": 0.0
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1074 },
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1075 "output.unsaved_changes":
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1076 {
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1077 "height": 100.0
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1078 },
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1079 "pinned_build_system": "",
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1080 "project": "duplex.sublime-project",
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1081 "replace":
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1082 {
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1083 "height": 46.0
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1084 },
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1085 "save_all_on_build": true,
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1086 "select_file":
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1087 {
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1088 "height": 0.0,
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1089 "last_filter": "",
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1090 "selected_items":
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1091 [
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1092 [
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1093 "",
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1094 "~/annex/Work/PSU/Nekrutenko/code/heteroplasmy/pipeline-meta.sh"
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1095 ]
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1096 ],
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1097 "width": 0.0
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1098 },
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1099 "select_project":
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1100 {
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1101 "height": 500.0,
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1102 "last_filter": "",
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1103 "selected_items":
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1104 [
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1105 ],
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1106 "width": 380.0
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1107 },
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1108 "select_symbol":
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1109 {
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1110 "height": 392.0,
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1111 "last_filter": "",
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1112 "selected_items":
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1113 [
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1114 [
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1115 "",
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1116 "fasta_format"
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1117 ]
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1118 ],
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1119 "width": 392.0
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1120 },
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1121 "selected_group": 0,
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1122 "settings":
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1123 {
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1124 },
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1125 "show_minimap": true,
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1126 "show_open_files": true,
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1127 "show_tabs": true,
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1128 "side_bar_visible": false,
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1129 "side_bar_width": 150.0,
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1130 "status_bar_visible": true,
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1131 "template_settings":
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1132 {
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1133 }
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1134 }