ngs_server 0.1 → 0.2

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Files changed (248) hide show
  1. data/bin/ngs_server +72 -50
  2. data/ext/bamtools/extconf.rb +3 -3
  3. data/ext/vcftools/Makefile +28 -0
  4. data/ext/vcftools/README.txt +36 -0
  5. data/ext/vcftools/cpp/.svn/all-wcprops +125 -0
  6. data/ext/vcftools/cpp/.svn/dir-prop-base +6 -0
  7. data/ext/vcftools/cpp/.svn/entries +708 -0
  8. data/ext/vcftools/cpp/.svn/text-base/Makefile.svn-base +46 -0
  9. data/ext/vcftools/cpp/.svn/text-base/dgeev.cpp.svn-base +146 -0
  10. data/ext/vcftools/cpp/.svn/text-base/dgeev.h.svn-base +43 -0
  11. data/ext/vcftools/cpp/.svn/text-base/output_log.cpp.svn-base +79 -0
  12. data/ext/vcftools/cpp/.svn/text-base/output_log.h.svn-base +34 -0
  13. data/ext/vcftools/cpp/.svn/text-base/parameters.cpp.svn-base +535 -0
  14. data/ext/vcftools/cpp/.svn/text-base/parameters.h.svn-base +154 -0
  15. data/ext/vcftools/cpp/.svn/text-base/vcf_entry.cpp.svn-base +497 -0
  16. data/ext/vcftools/cpp/.svn/text-base/vcf_entry.h.svn-base +190 -0
  17. data/ext/vcftools/cpp/.svn/text-base/vcf_entry_getters.cpp.svn-base +421 -0
  18. data/ext/vcftools/cpp/.svn/text-base/vcf_entry_setters.cpp.svn-base +482 -0
  19. data/ext/vcftools/cpp/.svn/text-base/vcf_file.cpp.svn-base +495 -0
  20. data/ext/vcftools/cpp/.svn/text-base/vcf_file.h.svn-base +184 -0
  21. data/ext/vcftools/cpp/.svn/text-base/vcf_file_diff.cpp.svn-base +1282 -0
  22. data/ext/vcftools/cpp/.svn/text-base/vcf_file_filters.cpp.svn-base +1215 -0
  23. data/ext/vcftools/cpp/.svn/text-base/vcf_file_format_convert.cpp.svn-base +1138 -0
  24. data/ext/vcftools/cpp/.svn/text-base/vcf_file_index.cpp.svn-base +171 -0
  25. data/ext/vcftools/cpp/.svn/text-base/vcf_file_output.cpp.svn-base +3012 -0
  26. data/ext/vcftools/cpp/.svn/text-base/vcftools.cpp.svn-base +107 -0
  27. data/ext/vcftools/cpp/.svn/text-base/vcftools.h.svn-base +25 -0
  28. data/ext/vcftools/cpp/Makefile +46 -0
  29. data/ext/vcftools/cpp/dgeev.cpp +146 -0
  30. data/ext/vcftools/cpp/dgeev.h +43 -0
  31. data/ext/vcftools/cpp/output_log.cpp +79 -0
  32. data/ext/vcftools/cpp/output_log.h +34 -0
  33. data/ext/vcftools/cpp/parameters.cpp +535 -0
  34. data/ext/vcftools/cpp/parameters.h +154 -0
  35. data/ext/vcftools/cpp/vcf_entry.cpp +497 -0
  36. data/ext/vcftools/cpp/vcf_entry.h +190 -0
  37. data/ext/vcftools/cpp/vcf_entry_getters.cpp +421 -0
  38. data/ext/vcftools/cpp/vcf_entry_setters.cpp +482 -0
  39. data/ext/vcftools/cpp/vcf_file.cpp +495 -0
  40. data/ext/vcftools/cpp/vcf_file.h +184 -0
  41. data/ext/vcftools/cpp/vcf_file_diff.cpp +1282 -0
  42. data/ext/vcftools/cpp/vcf_file_filters.cpp +1215 -0
  43. data/ext/vcftools/cpp/vcf_file_format_convert.cpp +1138 -0
  44. data/ext/vcftools/cpp/vcf_file_index.cpp +171 -0
  45. data/ext/vcftools/cpp/vcf_file_output.cpp +3012 -0
  46. data/ext/vcftools/cpp/vcftools.cpp +107 -0
  47. data/ext/vcftools/cpp/vcftools.h +25 -0
  48. data/ext/vcftools/examples/.svn/all-wcprops +185 -0
  49. data/ext/vcftools/examples/.svn/dir-prop-base +6 -0
  50. data/ext/vcftools/examples/.svn/entries +1048 -0
  51. data/ext/vcftools/examples/.svn/prop-base/perl-api-1.pl.svn-base +5 -0
  52. data/ext/vcftools/examples/.svn/text-base/annotate-test.vcf.svn-base +37 -0
  53. data/ext/vcftools/examples/.svn/text-base/annotate.out.svn-base +23 -0
  54. data/ext/vcftools/examples/.svn/text-base/annotate.txt.svn-base +7 -0
  55. data/ext/vcftools/examples/.svn/text-base/annotate2.out.svn-base +52 -0
  56. data/ext/vcftools/examples/.svn/text-base/annotate3.out.svn-base +23 -0
  57. data/ext/vcftools/examples/.svn/text-base/cmp-test-a-3.3.vcf.svn-base +12 -0
  58. data/ext/vcftools/examples/.svn/text-base/cmp-test-a.vcf.svn-base +12 -0
  59. data/ext/vcftools/examples/.svn/text-base/cmp-test-b-3.3.vcf.svn-base +12 -0
  60. data/ext/vcftools/examples/.svn/text-base/cmp-test-b.vcf.svn-base +12 -0
  61. data/ext/vcftools/examples/.svn/text-base/cmp-test.out.svn-base +53 -0
  62. data/ext/vcftools/examples/.svn/text-base/concat-a.vcf.svn-base +21 -0
  63. data/ext/vcftools/examples/.svn/text-base/concat-b.vcf.svn-base +13 -0
  64. data/ext/vcftools/examples/.svn/text-base/concat-c.vcf.svn-base +19 -0
  65. data/ext/vcftools/examples/.svn/text-base/concat.out.svn-base +39 -0
  66. data/ext/vcftools/examples/.svn/text-base/invalid-4.0.vcf.svn-base +31 -0
  67. data/ext/vcftools/examples/.svn/text-base/isec-n2-test.vcf.out.svn-base +19 -0
  68. data/ext/vcftools/examples/.svn/text-base/merge-test-a.vcf.svn-base +17 -0
  69. data/ext/vcftools/examples/.svn/text-base/merge-test-b.vcf.svn-base +17 -0
  70. data/ext/vcftools/examples/.svn/text-base/merge-test-c.vcf.svn-base +15 -0
  71. data/ext/vcftools/examples/.svn/text-base/merge-test.vcf.out.svn-base +31 -0
  72. data/ext/vcftools/examples/.svn/text-base/perl-api-1.pl.svn-base +46 -0
  73. data/ext/vcftools/examples/.svn/text-base/query-test.out.svn-base +6 -0
  74. data/ext/vcftools/examples/.svn/text-base/shuffle-test.vcf.svn-base +12 -0
  75. data/ext/vcftools/examples/.svn/text-base/subset.SNPs.out.svn-base +10 -0
  76. data/ext/vcftools/examples/.svn/text-base/subset.indels.out.svn-base +18 -0
  77. data/ext/vcftools/examples/.svn/text-base/subset.vcf.svn-base +21 -0
  78. data/ext/vcftools/examples/.svn/text-base/valid-3.3.vcf.svn-base +30 -0
  79. data/ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.stats.svn-base +104 -0
  80. data/ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.svn-base +34 -0
  81. data/ext/vcftools/examples/.svn/text-base/valid-4.1.vcf.svn-base +37 -0
  82. data/ext/vcftools/examples/annotate-test.vcf +37 -0
  83. data/ext/vcftools/examples/annotate.out +23 -0
  84. data/ext/vcftools/examples/annotate.txt +7 -0
  85. data/ext/vcftools/examples/annotate2.out +52 -0
  86. data/ext/vcftools/examples/annotate3.out +23 -0
  87. data/ext/vcftools/examples/cmp-test-a-3.3.vcf +12 -0
  88. data/ext/vcftools/examples/cmp-test-a.vcf +12 -0
  89. data/ext/vcftools/examples/cmp-test-b-3.3.vcf +12 -0
  90. data/ext/vcftools/examples/cmp-test-b.vcf +12 -0
  91. data/ext/vcftools/examples/cmp-test.out +53 -0
  92. data/ext/vcftools/examples/concat-a.vcf +21 -0
  93. data/ext/vcftools/examples/concat-b.vcf +13 -0
  94. data/ext/vcftools/examples/concat-c.vcf +19 -0
  95. data/ext/vcftools/examples/concat.out +39 -0
  96. data/ext/vcftools/examples/invalid-4.0.vcf +31 -0
  97. data/ext/vcftools/examples/isec-n2-test.vcf.out +19 -0
  98. data/ext/vcftools/examples/merge-test-a.vcf +17 -0
  99. data/ext/vcftools/examples/merge-test-b.vcf +17 -0
  100. data/ext/vcftools/examples/merge-test-c.vcf +15 -0
  101. data/ext/vcftools/examples/merge-test.vcf.out +31 -0
  102. data/ext/vcftools/examples/perl-api-1.pl +46 -0
  103. data/ext/vcftools/examples/query-test.out +6 -0
  104. data/ext/vcftools/examples/shuffle-test.vcf +12 -0
  105. data/ext/vcftools/examples/subset.SNPs.out +10 -0
  106. data/ext/vcftools/examples/subset.indels.out +18 -0
  107. data/ext/vcftools/examples/subset.vcf +21 -0
  108. data/ext/vcftools/examples/valid-3.3.vcf +30 -0
  109. data/ext/vcftools/examples/valid-4.0.vcf +34 -0
  110. data/ext/vcftools/examples/valid-4.0.vcf.stats +104 -0
  111. data/ext/vcftools/examples/valid-4.1.vcf +37 -0
  112. data/ext/vcftools/extconf.rb +2 -0
  113. data/ext/vcftools/perl/.svn/all-wcprops +149 -0
  114. data/ext/vcftools/perl/.svn/entries +844 -0
  115. data/ext/vcftools/perl/.svn/prop-base/fill-aa.svn-base +5 -0
  116. data/ext/vcftools/perl/.svn/prop-base/fill-an-ac.svn-base +5 -0
  117. data/ext/vcftools/perl/.svn/prop-base/fill-ref-md5.svn-base +5 -0
  118. data/ext/vcftools/perl/.svn/prop-base/tab-to-vcf.svn-base +5 -0
  119. data/ext/vcftools/perl/.svn/prop-base/test.t.svn-base +5 -0
  120. data/ext/vcftools/perl/.svn/prop-base/vcf-annotate.svn-base +5 -0
  121. data/ext/vcftools/perl/.svn/prop-base/vcf-compare.svn-base +5 -0
  122. data/ext/vcftools/perl/.svn/prop-base/vcf-concat.svn-base +5 -0
  123. data/ext/vcftools/perl/.svn/prop-base/vcf-convert.svn-base +5 -0
  124. data/ext/vcftools/perl/.svn/prop-base/vcf-fix-newlines.svn-base +5 -0
  125. data/ext/vcftools/perl/.svn/prop-base/vcf-isec.svn-base +5 -0
  126. data/ext/vcftools/perl/.svn/prop-base/vcf-merge.svn-base +5 -0
  127. data/ext/vcftools/perl/.svn/prop-base/vcf-query.svn-base +5 -0
  128. data/ext/vcftools/perl/.svn/prop-base/vcf-shuffle-cols.svn-base +5 -0
  129. data/ext/vcftools/perl/.svn/prop-base/vcf-sort.svn-base +5 -0
  130. data/ext/vcftools/perl/.svn/prop-base/vcf-stats.svn-base +5 -0
  131. data/ext/vcftools/perl/.svn/prop-base/vcf-subset.svn-base +5 -0
  132. data/ext/vcftools/perl/.svn/prop-base/vcf-to-tab.svn-base +5 -0
  133. data/ext/vcftools/perl/.svn/prop-base/vcf-validator.svn-base +5 -0
  134. data/ext/vcftools/perl/.svn/text-base/ChangeLog.svn-base +84 -0
  135. data/ext/vcftools/perl/.svn/text-base/FaSlice.pm.svn-base +214 -0
  136. data/ext/vcftools/perl/.svn/text-base/Makefile.svn-base +12 -0
  137. data/ext/vcftools/perl/.svn/text-base/Vcf.pm.svn-base +2853 -0
  138. data/ext/vcftools/perl/.svn/text-base/VcfStats.pm.svn-base +681 -0
  139. data/ext/vcftools/perl/.svn/text-base/fill-aa.svn-base +103 -0
  140. data/ext/vcftools/perl/.svn/text-base/fill-an-ac.svn-base +56 -0
  141. data/ext/vcftools/perl/.svn/text-base/fill-ref-md5.svn-base +204 -0
  142. data/ext/vcftools/perl/.svn/text-base/tab-to-vcf.svn-base +92 -0
  143. data/ext/vcftools/perl/.svn/text-base/test.t.svn-base +376 -0
  144. data/ext/vcftools/perl/.svn/text-base/vcf-annotate.svn-base +1099 -0
  145. data/ext/vcftools/perl/.svn/text-base/vcf-compare.svn-base +1193 -0
  146. data/ext/vcftools/perl/.svn/text-base/vcf-concat.svn-base +310 -0
  147. data/ext/vcftools/perl/.svn/text-base/vcf-convert.svn-base +180 -0
  148. data/ext/vcftools/perl/.svn/text-base/vcf-fix-newlines.svn-base +97 -0
  149. data/ext/vcftools/perl/.svn/text-base/vcf-isec.svn-base +660 -0
  150. data/ext/vcftools/perl/.svn/text-base/vcf-merge.svn-base +577 -0
  151. data/ext/vcftools/perl/.svn/text-base/vcf-query.svn-base +272 -0
  152. data/ext/vcftools/perl/.svn/text-base/vcf-shuffle-cols.svn-base +89 -0
  153. data/ext/vcftools/perl/.svn/text-base/vcf-sort.svn-base +79 -0
  154. data/ext/vcftools/perl/.svn/text-base/vcf-stats.svn-base +160 -0
  155. data/ext/vcftools/perl/.svn/text-base/vcf-subset.svn-base +206 -0
  156. data/ext/vcftools/perl/.svn/text-base/vcf-to-tab.svn-base +112 -0
  157. data/ext/vcftools/perl/.svn/text-base/vcf-validator.svn-base +145 -0
  158. data/ext/vcftools/perl/ChangeLog +84 -0
  159. data/ext/vcftools/perl/FaSlice.pm +214 -0
  160. data/ext/vcftools/perl/Makefile +12 -0
  161. data/ext/vcftools/perl/Vcf.pm +2853 -0
  162. data/ext/vcftools/perl/VcfStats.pm +681 -0
  163. data/ext/vcftools/perl/fill-aa +103 -0
  164. data/ext/vcftools/perl/fill-an-ac +56 -0
  165. data/ext/vcftools/perl/fill-ref-md5 +204 -0
  166. data/ext/vcftools/perl/tab-to-vcf +92 -0
  167. data/ext/vcftools/perl/test.t +376 -0
  168. data/ext/vcftools/perl/vcf-annotate +1099 -0
  169. data/ext/vcftools/perl/vcf-compare +1193 -0
  170. data/ext/vcftools/perl/vcf-concat +310 -0
  171. data/ext/vcftools/perl/vcf-convert +180 -0
  172. data/ext/vcftools/perl/vcf-fix-newlines +97 -0
  173. data/ext/vcftools/perl/vcf-isec +660 -0
  174. data/ext/vcftools/perl/vcf-merge +577 -0
  175. data/ext/vcftools/perl/vcf-query +286 -0
  176. data/ext/vcftools/perl/vcf-shuffle-cols +89 -0
  177. data/ext/vcftools/perl/vcf-sort +79 -0
  178. data/ext/vcftools/perl/vcf-stats +160 -0
  179. data/ext/vcftools/perl/vcf-subset +206 -0
  180. data/ext/vcftools/perl/vcf-to-tab +112 -0
  181. data/ext/vcftools/perl/vcf-validator +145 -0
  182. data/ext/vcftools/website/.svn/all-wcprops +41 -0
  183. data/ext/vcftools/website/.svn/entries +238 -0
  184. data/ext/vcftools/website/.svn/prop-base/VCF-poster.pdf.svn-base +5 -0
  185. data/ext/vcftools/website/.svn/prop-base/favicon.ico.svn-base +5 -0
  186. data/ext/vcftools/website/.svn/prop-base/favicon.png.svn-base +5 -0
  187. data/ext/vcftools/website/.svn/text-base/Makefile.svn-base +6 -0
  188. data/ext/vcftools/website/.svn/text-base/README.svn-base +2 -0
  189. data/ext/vcftools/website/.svn/text-base/VCF-poster.pdf.svn-base +0 -0
  190. data/ext/vcftools/website/.svn/text-base/default.css.svn-base +250 -0
  191. data/ext/vcftools/website/.svn/text-base/favicon.ico.svn-base +0 -0
  192. data/ext/vcftools/website/.svn/text-base/favicon.png.svn-base +0 -0
  193. data/ext/vcftools/website/Makefile +6 -0
  194. data/ext/vcftools/website/README +2 -0
  195. data/ext/vcftools/website/VCF-poster.pdf +0 -0
  196. data/ext/vcftools/website/default.css +250 -0
  197. data/ext/vcftools/website/favicon.ico +0 -0
  198. data/ext/vcftools/website/favicon.png +0 -0
  199. data/ext/vcftools/website/img/.svn/all-wcprops +53 -0
  200. data/ext/vcftools/website/img/.svn/entries +300 -0
  201. data/ext/vcftools/website/img/.svn/prop-base/bg.gif.svn-base +5 -0
  202. data/ext/vcftools/website/img/.svn/prop-base/bgcode.gif.svn-base +5 -0
  203. data/ext/vcftools/website/img/.svn/prop-base/bgcontainer.gif.svn-base +5 -0
  204. data/ext/vcftools/website/img/.svn/prop-base/bgul.gif.svn-base +5 -0
  205. data/ext/vcftools/website/img/.svn/prop-base/header.gif.svn-base +5 -0
  206. data/ext/vcftools/website/img/.svn/prop-base/li.gif.svn-base +5 -0
  207. data/ext/vcftools/website/img/.svn/prop-base/quote.gif.svn-base +5 -0
  208. data/ext/vcftools/website/img/.svn/prop-base/search.gif.svn-base +5 -0
  209. data/ext/vcftools/website/img/.svn/text-base/bg.gif.svn-base +0 -0
  210. data/ext/vcftools/website/img/.svn/text-base/bgcode.gif.svn-base +0 -0
  211. data/ext/vcftools/website/img/.svn/text-base/bgcontainer.gif.svn-base +0 -0
  212. data/ext/vcftools/website/img/.svn/text-base/bgul.gif.svn-base +0 -0
  213. data/ext/vcftools/website/img/.svn/text-base/header.gif.svn-base +0 -0
  214. data/ext/vcftools/website/img/.svn/text-base/li.gif.svn-base +0 -0
  215. data/ext/vcftools/website/img/.svn/text-base/quote.gif.svn-base +0 -0
  216. data/ext/vcftools/website/img/.svn/text-base/search.gif.svn-base +0 -0
  217. data/ext/vcftools/website/img/bg.gif +0 -0
  218. data/ext/vcftools/website/img/bgcode.gif +0 -0
  219. data/ext/vcftools/website/img/bgcontainer.gif +0 -0
  220. data/ext/vcftools/website/img/bgul.gif +0 -0
  221. data/ext/vcftools/website/img/header.gif +0 -0
  222. data/ext/vcftools/website/img/li.gif +0 -0
  223. data/ext/vcftools/website/img/quote.gif +0 -0
  224. data/ext/vcftools/website/img/search.gif +0 -0
  225. data/ext/vcftools/website/src/.svn/all-wcprops +53 -0
  226. data/ext/vcftools/website/src/.svn/entries +300 -0
  227. data/ext/vcftools/website/src/.svn/text-base/docs.inc.svn-base +202 -0
  228. data/ext/vcftools/website/src/.svn/text-base/index.inc.svn-base +52 -0
  229. data/ext/vcftools/website/src/.svn/text-base/index.php.svn-base +80 -0
  230. data/ext/vcftools/website/src/.svn/text-base/license.inc.svn-base +27 -0
  231. data/ext/vcftools/website/src/.svn/text-base/links.inc.svn-base +13 -0
  232. data/ext/vcftools/website/src/.svn/text-base/options.inc.svn-base +654 -0
  233. data/ext/vcftools/website/src/.svn/text-base/perl_module.inc.svn-base +249 -0
  234. data/ext/vcftools/website/src/.svn/text-base/specs.inc.svn-base +18 -0
  235. data/ext/vcftools/website/src/docs.inc +202 -0
  236. data/ext/vcftools/website/src/index.inc +52 -0
  237. data/ext/vcftools/website/src/index.php +80 -0
  238. data/ext/vcftools/website/src/license.inc +27 -0
  239. data/ext/vcftools/website/src/links.inc +13 -0
  240. data/ext/vcftools/website/src/options.inc +654 -0
  241. data/ext/vcftools/website/src/perl_module.inc +249 -0
  242. data/ext/vcftools/website/src/specs.inc +18 -0
  243. data/lib/config.ru +9 -0
  244. data/lib/ngs_server/add.rb +9 -0
  245. data/lib/ngs_server/version.rb +1 -1
  246. data/lib/ngs_server.rb +55 -3
  247. data/ngs_server.gemspec +5 -2
  248. metadata +296 -6
data/ext/vcftools/website/src/.svn/text-base/license.inc.svn-base ADDED
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+
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+ <div class="item">
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+ <h1>License</h1>
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+ <p>The program package is released under the GNU General Public License version 3.0 (GPLv3).</p>
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+ </div>
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+
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+ <div class="item">
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+ <h1>Citing VCFtools</h1>
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+ <p>If you make use of VCFtools in your research, we would appreciate a citation of the following
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+ paper:<br><br>
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+ <a href="http://dx.doi.org/10.1093/bioinformatics/btr330"><i>The Variant Call Format and VCFtools</i></a>,
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+ Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo,
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+ Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin
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+ and 1000 Genomes Project Analysis Group, <b>Bioinformatics</b>, 2011
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+ </p>
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+ </div>
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+
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+ <div class="item">
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+ <h1>Authors</h1>
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+ <p>The program package is maintained and developed by</p>
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+ <ul>
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+ <li> <a href="http://www.adamauton.com/">Adam Auton</a> (C++ Module)
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+ <li> Petr Danecek (Perl Module)
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+ </ul>
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+ </div>
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+
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data/ext/vcftools/website/src/.svn/text-base/links.inc.svn-base ADDED
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+ <h1>VCF related links</h1>
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+ <p>If you know of any other VCF-related resources, please let us know.</p>
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+ <li><a href="http://sourceforge.net/projects/samtools/files/tabix/">tabix</a> - Tabix is an indexing tool that is required for certain features in VCFtools. </a>
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+ <li><a href="https://github.com/ekg/vcflib">vcflib</a> - A simple C++ library for parsing and manipulating VCF files from Erik Garrison. </a></li>
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+ <li><a href="https://github.com/indapa/VcfPythonUtils">VcfPythonUtils</a> - Some Python utilities to work with VCF from Amit Indap. </a></li>
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+ <li><a href="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit">The Genome Analysis Toolkit</a> - The GATK Java package from the Broad includes a number of routines for generating and manipulating VCF file.</a></li>
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+ <li><a href="https://github.com/AlistairNWard/vcfCTools">vcfCTools</a> - C++ implementation of vcfPytools from Alistair Ward.
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+ </div>
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