genoverse 3.2.0 → 4.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (217) hide show
  1. package/.eslintrc.js +93 -162
  2. package/.github/workflows/test.yml +9 -10
  3. package/.github/workflows/update-gh-pages.yml +33 -0
  4. package/LICENSE.TXT +2 -2
  5. package/README.md +174 -3
  6. package/{i → assets}/sort_handle.png +0 -0
  7. package/babel.config.js +19 -0
  8. package/dist/129.css +334 -0
  9. package/dist/129.css.map +1 -0
  10. package/dist/129.genoverse.js +2 -0
  11. package/dist/129.genoverse.js.map +1 -0
  12. package/dist/15d98c18221c8bcb2334.ttf +0 -0
  13. package/dist/166.css +2 -0
  14. package/dist/166.genoverse.js +1 -0
  15. package/dist/216.css +20 -0
  16. package/dist/216.css.map +1 -0
  17. package/dist/232.css +114 -0
  18. package/dist/232.css.map +1 -0
  19. package/dist/232.genoverse.js +2 -0
  20. package/dist/232.genoverse.js.map +1 -0
  21. package/dist/2e659e443f3e98569e9f.png +0 -0
  22. package/dist/394.css +114 -0
  23. package/dist/394.css.map +1 -0
  24. package/dist/394.genoverse.js +2 -0
  25. package/dist/394.genoverse.js.map +1 -0
  26. package/dist/469.css +24 -0
  27. package/dist/469.css.map +1 -0
  28. package/dist/469.genoverse.js +2 -0
  29. package/dist/469.genoverse.js.map +1 -0
  30. package/dist/4896d4b04430cc3dfb06.woff2 +0 -0
  31. package/dist/530.css +39 -0
  32. package/dist/530.css.map +1 -0
  33. package/dist/530.genoverse.js +2 -0
  34. package/dist/530.genoverse.js.map +1 -0
  35. package/dist/547.css +469 -0
  36. package/dist/547.css.map +1 -0
  37. package/dist/547.genoverse.js +1 -0
  38. package/dist/729.css +315 -0
  39. package/dist/729.css.map +1 -0
  40. package/dist/79da213423ac0def2058.ttf +0 -0
  41. package/dist/804.genoverse.js +2 -0
  42. package/dist/804.genoverse.js.map +1 -0
  43. package/dist/842.genoverse.js +2 -0
  44. package/dist/842.genoverse.js.map +1 -0
  45. package/dist/893.genoverse.js +2 -0
  46. package/dist/893.genoverse.js.map +1 -0
  47. package/dist/949.css +315 -0
  48. package/dist/949.css.map +1 -0
  49. package/dist/949.genoverse.js +2 -0
  50. package/dist/949.genoverse.js.map +1 -0
  51. package/dist/952.css +315 -0
  52. package/dist/952.css.map +1 -0
  53. package/dist/952.genoverse.js +2 -0
  54. package/dist/952.genoverse.js.map +1 -0
  55. package/dist/d79c2ec96ab9ff1161a2.woff2 +0 -0
  56. package/dist/genoverse.js +2 -0
  57. package/dist/genoverse.js.map +1 -0
  58. package/index.html +13 -14
  59. package/jest.config.js +5 -0
  60. package/jest.setup.js +13 -0
  61. package/package.json +29 -12
  62. package/{css → src/css}/controlPanel.css +0 -0
  63. package/{css → src/css}/fileDrop.css +0 -0
  64. package/src/css/fontawesome.css +3 -0
  65. package/{css → src/css}/fullscreen.css +0 -0
  66. package/{css → src/css}/genoverse.css +1 -1
  67. package/{css → src/css}/karyotype.css +2 -0
  68. package/{css → src/css}/resizer.css +0 -0
  69. package/{css → src/css}/tooltips.css +0 -0
  70. package/{css → src/css}/trackControls.css +0 -0
  71. package/src/js/Genoverse.js +1747 -0
  72. package/{js → src/js}/Track/Controller/Sequence.js +6 -4
  73. package/src/js/Track/Controller/Stranded.js +83 -0
  74. package/{js → src/js}/Track/Controller.js +201 -160
  75. package/src/js/Track/Model/File/BAM.js +47 -0
  76. package/src/js/Track/Model/File/BED.js +122 -0
  77. package/src/js/Track/Model/File/GFF.js +42 -0
  78. package/src/js/Track/Model/File/VCF.js +109 -0
  79. package/src/js/Track/Model/File/WIG.js +82 -0
  80. package/src/js/Track/Model/File.js +36 -0
  81. package/src/js/Track/Model/Gene/Ensembl.js +24 -0
  82. package/{js → src/js}/Track/Model/Gene.js +3 -1
  83. package/src/js/Track/Model/Sequence/Ensembl.js +6 -0
  84. package/{js → src/js}/Track/Model/Sequence/Fasta.js +24 -17
  85. package/{js → src/js}/Track/Model/Sequence.js +10 -7
  86. package/{js → src/js}/Track/Model/SequenceVariation.js +17 -11
  87. package/{js → src/js}/Track/Model/Stranded.js +11 -8
  88. package/src/js/Track/Model/Transcript/Ensembl.js +73 -0
  89. package/{js → src/js}/Track/Model/Transcript.js +3 -1
  90. package/{js → src/js}/Track/Model.js +125 -93
  91. package/{js → src/js}/Track/View/Gene/Ensembl.js +6 -4
  92. package/src/js/Track/View/Gene.js +8 -0
  93. package/{js → src/js}/Track/View/Sequence.js +18 -22
  94. package/src/js/Track/View/SequenceVariation.js +117 -0
  95. package/src/js/Track/View/Transcript/Ensembl.js +17 -0
  96. package/src/js/Track/View/Transcript.js +32 -0
  97. package/{js → src/js}/Track/View.js +200 -159
  98. package/{js → src/js}/Track/library/Chromosome.js +18 -13
  99. package/src/js/Track/library/File/BAM.js +34 -0
  100. package/src/js/Track/library/File/BED.js +27 -0
  101. package/src/js/Track/library/File/BIGBED.js +51 -0
  102. package/src/js/Track/library/File/BIGWIG.js +54 -0
  103. package/src/js/Track/library/File/GFF.js +10 -0
  104. package/{js → src/js}/Track/library/File/VCF.js +29 -22
  105. package/src/js/Track/library/File/WIG.js +8 -0
  106. package/{js → src/js}/Track/library/File.js +4 -2
  107. package/src/js/Track/library/Gene.js +44 -0
  108. package/src/js/Track/library/Graph/Bar.js +263 -0
  109. package/src/js/Track/library/Graph/Line.js +335 -0
  110. package/{js → src/js}/Track/library/Graph.js +137 -114
  111. package/{js → src/js}/Track/library/HighlightRegion.js +118 -93
  112. package/src/js/Track/library/Legend.js +258 -0
  113. package/{js → src/js}/Track/library/Scalebar.js +69 -49
  114. package/{js → src/js}/Track/library/Scaleline.js +29 -27
  115. package/src/js/Track/library/Static.js +82 -0
  116. package/{js → src/js}/Track/library/dbSNP.js +47 -50
  117. package/src/js/Track.js +651 -0
  118. package/{js → src/js}/genomes/grch37.js +52 -52
  119. package/{js → src/js}/genomes/grch38.js +52 -52
  120. package/src/js/lib/BWReader.js +562 -0
  121. package/src/js/lib/VCFReader.js +296 -0
  122. package/src/js/lib/dalliance/bam.js +517 -0
  123. package/src/js/lib/dalliance/bin.js +317 -0
  124. package/src/js/lib/dalliance/jszlib-inflate.js +2159 -0
  125. package/src/js/lib/dalliance/lh3utils.js +105 -0
  126. package/src/js/lib/dalliance/sha1.js +334 -0
  127. package/src/js/lib/import-tracks.js +42 -0
  128. package/{js/lib → src/js/lib/jquery-plugins}/jquery.mousehold.js +0 -0
  129. package/{js/lib → src/js/lib/jquery-plugins}/jquery.mousewheel.js +0 -0
  130. package/{js/lib → src/js/lib/jquery-plugins}/jquery.tipsy.js +0 -0
  131. package/src/js/lib/jquery.js +26 -0
  132. package/src/js/lib/polyfills.js +11 -0
  133. package/src/js/lib/wrap-functions.js +88 -0
  134. package/src/js/plugins/controlPanel.js +388 -0
  135. package/src/js/plugins/fileDrop.js +81 -0
  136. package/src/js/plugins/focusRegion.js +13 -0
  137. package/{js → src/js}/plugins/fullscreen.js +18 -14
  138. package/{js → src/js}/plugins/karyotype.js +51 -45
  139. package/src/js/plugins/resizer.js +52 -0
  140. package/{js → src/js}/plugins/tooltips.js +31 -29
  141. package/src/js/plugins/trackControls.js +159 -0
  142. package/test/View/render-legends.test.js +1 -1
  143. package/test/change-width.test.js +71 -0
  144. package/test/create-and-destroy.test.js +2 -2
  145. package/test/track-ordering.test.js +3 -2
  146. package/test/track_config/config-settings.test.js +1 -1
  147. package/test/utils.js +4 -2
  148. package/webpack.config.js +103 -34
  149. package/css/font-awesome.css +0 -3
  150. package/expanded.html +0 -120
  151. package/fontawesome/css/fontawesome.min.css +0 -5
  152. package/fontawesome/css/regular.min.css +0 -5
  153. package/fontawesome/css/solid.min.css +0 -5
  154. package/fontawesome/webfonts/fa-brands-400.ttf +0 -0
  155. package/fontawesome/webfonts/fa-brands-400.woff +0 -0
  156. package/fontawesome/webfonts/fa-brands-400.woff2 +0 -0
  157. package/fontawesome/webfonts/fa-regular-400.ttf +0 -0
  158. package/fontawesome/webfonts/fa-regular-400.woff +0 -0
  159. package/fontawesome/webfonts/fa-regular-400.woff2 +0 -0
  160. package/fontawesome/webfonts/fa-solid-900.ttf +0 -0
  161. package/fontawesome/webfonts/fa-solid-900.woff +0 -0
  162. package/fontawesome/webfonts/fa-solid-900.woff2 +0 -0
  163. package/help.pdf +0 -0
  164. package/index.js +0 -83
  165. package/js/Genoverse.js +0 -1681
  166. package/js/Track/Controller/Stranded.js +0 -73
  167. package/js/Track/Model/File/BAM.js +0 -44
  168. package/js/Track/Model/File/BED.js +0 -116
  169. package/js/Track/Model/File/GFF.js +0 -40
  170. package/js/Track/Model/File/VCF.js +0 -101
  171. package/js/Track/Model/File/WIG.js +0 -67
  172. package/js/Track/Model/File.js +0 -36
  173. package/js/Track/Model/Gene/Ensembl.js +0 -22
  174. package/js/Track/Model/Sequence/Ensembl.js +0 -4
  175. package/js/Track/Model/Transcript/Ensembl.js +0 -67
  176. package/js/Track/View/Gene.js +0 -6
  177. package/js/Track/View/Sequence/Variation.js +0 -115
  178. package/js/Track/View/Transcript/Ensembl.js +0 -12
  179. package/js/Track/View/Transcript.js +0 -28
  180. package/js/Track/library/File/BAM.js +0 -30
  181. package/js/Track/library/File/BED.js +0 -24
  182. package/js/Track/library/File/BIGBED.js +0 -47
  183. package/js/Track/library/File/BIGWIG.js +0 -52
  184. package/js/Track/library/File/GFF.js +0 -9
  185. package/js/Track/library/File/WIG.js +0 -5
  186. package/js/Track/library/Gene.js +0 -37
  187. package/js/Track/library/Graph/Bar.js +0 -235
  188. package/js/Track/library/Graph/Line.js +0 -296
  189. package/js/Track/library/Legend.js +0 -224
  190. package/js/Track/library/Static.js +0 -78
  191. package/js/Track.js +0 -632
  192. package/js/genoverse.min.js +0 -2
  193. package/js/genoverse.min.js.map +0 -1
  194. package/js/lib/BWReader.js +0 -578
  195. package/js/lib/Base.js +0 -145
  196. package/js/lib/VCFReader.js +0 -286
  197. package/js/lib/dalliance/js/bam.js +0 -494
  198. package/js/lib/dalliance/js/bin.js +0 -185
  199. package/js/lib/dalliance/js/das.js +0 -749
  200. package/js/lib/dalliance/js/utils.js +0 -370
  201. package/js/lib/dalliance-lib.js +0 -3594
  202. package/js/lib/dalliance-lib.min.js +0 -68
  203. package/js/lib/jDataView.js +0 -2
  204. package/js/lib/jParser.js +0 -192
  205. package/js/lib/jquery-ui.js +0 -8
  206. package/js/lib/jquery.js +0 -2
  207. package/js/lib/rtree.js +0 -1
  208. package/js/plugins/controlPanel.js +0 -395
  209. package/js/plugins/fileDrop.js +0 -62
  210. package/js/plugins/focusRegion.js +0 -12
  211. package/js/plugins/resizer.js +0 -45
  212. package/js/plugins/trackControls.js +0 -143
  213. package/utils/expandedTemplate.html +0 -46
  214. package/utils/git-hooks/post-commit +0 -9
  215. package/utils/git-hooks/pre-commit +0 -7
  216. package/utils/git-hooks/setup +0 -6
  217. package/utils/makeExpanded.js +0 -19
package/utils/expandedTemplate.html DELETED
@@ -1,46 +0,0 @@
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- <!DOCTYPE HTML>
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- <html>
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- <head>
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- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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-
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- __CSS__
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- </head>
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- <body>
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- <div id="genoverse"></div>
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-
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- __JS__
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-
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- <script>
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- window.genoverse = new Genoverse({
15
- container : '#genoverse',
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- width : 800,
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- genome : 'GRCh38',
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- chr : 13,
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- start : 32296945,
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- end : 32370557,
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- plugins : [ 'controlPanel', [ 'karyotype', { showAssembly: true }], 'trackControls', 'resizer', 'focusRegion', 'fullscreen', 'tooltips', 'fileDrop' ],
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- tracks : [
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- Genoverse.Track.Scaleline.extend({ strand: false }),
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- Genoverse.Track.Scalebar,
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- Genoverse.Track.extend({
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- name : 'Sequence',
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- controller : Genoverse.Track.Controller.Sequence,
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- model : Genoverse.Track.Model.Sequence.Ensembl,
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- view : Genoverse.Track.View.Sequence,
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- resizable : 'auto',
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- 100000 : false
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- }),
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- Genoverse.Track.Gene,
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- Genoverse.Track.extend({
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- name : 'Regulatory Features',
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- url : '//rest.ensembl.org/overlap/region/human/__CHR__:__START__-__END__?feature=regulatory;content-type=application/json',
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- resizable : 'auto',
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- model : Genoverse.Track.Model.extend({ dataRequestLimit : 5000000 }),
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- setFeatureColor : function (f) { f.color = '#AAA'; }
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- }),
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- Genoverse.Track.dbSNP
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- ]
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- });
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- </script>
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- </body>
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- </html>
package/utils/git-hooks/post-commit DELETED
@@ -1,9 +0,0 @@
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- #!/bin/bash
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-
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- git stash apply -q;
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- git stash drop -q;
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-
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- if [[ $( git status | grep 'Unmerged paths' ) ]]
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- then
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- git status
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- fi
package/utils/git-hooks/pre-commit DELETED
@@ -1,7 +0,0 @@
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- #!/bin/bash
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-
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- git stash -k -q
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- yarn build || exit 1
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- git add js/genoverse.min.js
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- git add js/genoverse.min.js.map
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- git add expanded.html
package/utils/git-hooks/setup DELETED
@@ -1,6 +0,0 @@
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- #!/bin/bash
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-
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- cd "$( dirname "${BASH_SOURCE[0]}" )" && cd ../..; # cd to the Genoverse directory
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-
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- ln -sfT "$( pwd )/utils/git-hooks/pre-commit" .git/hooks/pre-commit;
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- ln -sfT "$( pwd )/utils/git-hooks/post-commit" .git/hooks/post-commit;
package/utils/makeExpanded.js DELETED
@@ -1,19 +0,0 @@
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- const fs = require('fs');
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-
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- const dir = process.cwd();
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-
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- const jsFiles = fs.readFileSync(`${dir}/index.js`, 'utf8').split('\n').filter(
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- t => /require/.test(t)
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- ).map(
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- t => `<script type="text/javascript" src="${t.replace(/.*require\((.+)\).*/, '$1').replace(/__dirname/, '').replace(/[+\s\\']/g, '').replace(/^\//, '')}"></script>`
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- );
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-
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- const cssFiles = fs.readdirSync(`${dir}/css`).sort(
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- (a, b) => (b.match(/^genoverse.css$/) || []).length - (a.match(/^genoverse.css$/) || []).length // genoverse.css must go first, but order is not important for other files since all plugins are namespaced
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- ).map(
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- file => `<link rel="stylesheet" type="text/css" href="css/${file}" />`
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- );
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-
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- const html = fs.readFileSync(`${dir}/utils/expandedTemplate.html`, 'utf8').replace(/__JS__/, jsFiles.join('\n ')).replace(/__CSS__/, cssFiles.join('\n '));
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-
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- fs.writeFileSync(`${dir}/expanded.html`, html, 'utf8');