ngs_server 0.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (284) hide show
  1. data/.gitignore +4 -0
  2. data/Gemfile +4 -0
  3. data/Rakefile +2 -0
  4. data/bin/ngs_server +58 -0
  5. data/data/holder.txt +0 -0
  6. data/ext/bamtools/CMakeLists.txt +49 -0
  7. data/ext/bamtools/LICENSE +22 -0
  8. data/ext/bamtools/README +60 -0
  9. data/ext/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf +0 -0
  10. data/ext/bamtools/docs/Doxyfile +1601 -0
  11. data/ext/bamtools/extconf.rb +9 -0
  12. data/ext/bamtools/src/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
  13. data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake +13 -0
  14. data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/build.make +65 -0
  15. data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/cmake_clean.cmake +8 -0
  16. data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/depend.internal +3 -0
  17. data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/depend.make +3 -0
  18. data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/progress.make +2 -0
  19. data/ext/bamtools/src/CMakeFiles/progress.marks +1 -0
  20. data/ext/bamtools/src/CMakeLists.txt +18 -0
  21. data/ext/bamtools/src/ExportHeader.cmake +31 -0
  22. data/ext/bamtools/src/Makefile +182 -0
  23. data/ext/bamtools/src/api/BamAlignment.cpp +2432 -0
  24. data/ext/bamtools/src/api/BamAlignment.h +206 -0
  25. data/ext/bamtools/src/api/BamAux.h +456 -0
  26. data/ext/bamtools/src/api/BamConstants.h +127 -0
  27. data/ext/bamtools/src/api/BamIndex.h +79 -0
  28. data/ext/bamtools/src/api/BamMultiReader.cpp +395 -0
  29. data/ext/bamtools/src/api/BamMultiReader.h +126 -0
  30. data/ext/bamtools/src/api/BamReader.cpp +369 -0
  31. data/ext/bamtools/src/api/BamReader.h +117 -0
  32. data/ext/bamtools/src/api/BamWriter.cpp +142 -0
  33. data/ext/bamtools/src/api/BamWriter.h +63 -0
  34. data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake +14 -0
  35. data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/build.make +80 -0
  36. data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/cmake_clean.cmake +8 -0
  37. data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/depend.internal +3 -0
  38. data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/depend.make +3 -0
  39. data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/progress.make +2 -0
  40. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o +0 -0
  41. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o +0 -0
  42. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o +0 -0
  43. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o +0 -0
  44. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/CXX.includecache +596 -0
  45. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/DependInfo.cmake +41 -0
  46. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o +0 -0
  47. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o +0 -0
  48. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o +0 -0
  49. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o +0 -0
  50. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o +0 -0
  51. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o +0 -0
  52. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o +0 -0
  53. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/build.make +675 -0
  54. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/cmake_clean.cmake +32 -0
  55. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/cmake_clean_target.cmake +3 -0
  56. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/depend.internal +295 -0
  57. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/depend.make +295 -0
  58. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/flags.make +8 -0
  59. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamHeader_p.cpp.o +0 -0
  60. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamIndexFactory_p.cpp.o +0 -0
  61. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamMultiReader_p.cpp.o +0 -0
  62. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamRandomAccessController_p.cpp.o +0 -0
  63. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamReader_p.cpp.o +0 -0
  64. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamStandardIndex_p.cpp.o +0 -0
  65. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamToolsIndex_p.cpp.o +0 -0
  66. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamWriter_p.cpp.o +0 -0
  67. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BgzfStream_p.cpp.o +0 -0
  68. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/SamFormatParser_p.cpp.o +0 -0
  69. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/SamFormatPrinter_p.cpp.o +0 -0
  70. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/SamHeaderValidator_p.cpp.o +0 -0
  71. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/link.txt +2 -0
  72. data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/progress.make +24 -0
  73. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o +0 -0
  74. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o +0 -0
  75. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o +0 -0
  76. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o +0 -0
  77. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/CXX.includecache +596 -0
  78. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake +47 -0
  79. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o +0 -0
  80. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o +0 -0
  81. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o +0 -0
  82. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o +0 -0
  83. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o +0 -0
  84. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o +0 -0
  85. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o +0 -0
  86. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/build.make +677 -0
  87. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/cmake_clean.cmake +33 -0
  88. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/depend.internal +295 -0
  89. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/depend.make +295 -0
  90. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/flags.make +8 -0
  91. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamHeader_p.cpp.o +0 -0
  92. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamIndexFactory_p.cpp.o +0 -0
  93. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamMultiReader_p.cpp.o +0 -0
  94. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamRandomAccessController_p.cpp.o +0 -0
  95. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamReader_p.cpp.o +0 -0
  96. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamStandardIndex_p.cpp.o +0 -0
  97. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamToolsIndex_p.cpp.o +0 -0
  98. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamWriter_p.cpp.o +0 -0
  99. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BgzfStream_p.cpp.o +0 -0
  100. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamFormatParser_p.cpp.o +0 -0
  101. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamFormatPrinter_p.cpp.o +0 -0
  102. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamHeaderValidator_p.cpp.o +0 -0
  103. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/link.txt +1 -0
  104. data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/progress.make +24 -0
  105. data/ext/bamtools/src/api/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
  106. data/ext/bamtools/src/api/CMakeFiles/progress.marks +1 -0
  107. data/ext/bamtools/src/api/CMakeLists.txt +78 -0
  108. data/ext/bamtools/src/api/Makefile +902 -0
  109. data/ext/bamtools/src/api/SamConstants.h +95 -0
  110. data/ext/bamtools/src/api/SamHeader.cpp +184 -0
  111. data/ext/bamtools/src/api/SamHeader.h +68 -0
  112. data/ext/bamtools/src/api/SamProgram.cpp +139 -0
  113. data/ext/bamtools/src/api/SamProgram.h +61 -0
  114. data/ext/bamtools/src/api/SamProgramChain.cpp +351 -0
  115. data/ext/bamtools/src/api/SamProgramChain.h +85 -0
  116. data/ext/bamtools/src/api/SamReadGroup.cpp +221 -0
  117. data/ext/bamtools/src/api/SamReadGroup.h +68 -0
  118. data/ext/bamtools/src/api/SamReadGroupDictionary.cpp +289 -0
  119. data/ext/bamtools/src/api/SamReadGroupDictionary.h +86 -0
  120. data/ext/bamtools/src/api/SamSequence.cpp +161 -0
  121. data/ext/bamtools/src/api/SamSequence.h +60 -0
  122. data/ext/bamtools/src/api/SamSequenceDictionary.cpp +292 -0
  123. data/ext/bamtools/src/api/SamSequenceDictionary.h +88 -0
  124. data/ext/bamtools/src/api/api_global.h +21 -0
  125. data/ext/bamtools/src/api/cmake_install.cmake +122 -0
  126. data/ext/bamtools/src/api/internal/BamHeader_p.cpp +132 -0
  127. data/ext/bamtools/src/api/internal/BamHeader_p.h +71 -0
  128. data/ext/bamtools/src/api/internal/BamIndexFactory_p.cpp +112 -0
  129. data/ext/bamtools/src/api/internal/BamIndexFactory_p.h +49 -0
  130. data/ext/bamtools/src/api/internal/BamMultiMerger_p.h +297 -0
  131. data/ext/bamtools/src/api/internal/BamMultiReader_p.cpp +805 -0
  132. data/ext/bamtools/src/api/internal/BamMultiReader_p.h +103 -0
  133. data/ext/bamtools/src/api/internal/BamRandomAccessController_p.cpp +272 -0
  134. data/ext/bamtools/src/api/internal/BamRandomAccessController_p.h +93 -0
  135. data/ext/bamtools/src/api/internal/BamReader_p.cpp +380 -0
  136. data/ext/bamtools/src/api/internal/BamReader_p.h +112 -0
  137. data/ext/bamtools/src/api/internal/BamStandardIndex_p.cpp +986 -0
  138. data/ext/bamtools/src/api/internal/BamStandardIndex_p.h +236 -0
  139. data/ext/bamtools/src/api/internal/BamToolsIndex_p.cpp +641 -0
  140. data/ext/bamtools/src/api/internal/BamToolsIndex_p.h +187 -0
  141. data/ext/bamtools/src/api/internal/BamWriter_p.cpp +424 -0
  142. data/ext/bamtools/src/api/internal/BamWriter_p.h +66 -0
  143. data/ext/bamtools/src/api/internal/BgzfStream_p.cpp +438 -0
  144. data/ext/bamtools/src/api/internal/BgzfStream_p.h +108 -0
  145. data/ext/bamtools/src/api/internal/SamFormatParser_p.cpp +230 -0
  146. data/ext/bamtools/src/api/internal/SamFormatParser_p.h +61 -0
  147. data/ext/bamtools/src/api/internal/SamFormatPrinter_p.cpp +210 -0
  148. data/ext/bamtools/src/api/internal/SamFormatPrinter_p.h +60 -0
  149. data/ext/bamtools/src/api/internal/SamHeaderValidator_p.cpp +510 -0
  150. data/ext/bamtools/src/api/internal/SamHeaderValidator_p.h +101 -0
  151. data/ext/bamtools/src/api/internal/SamHeaderVersion_p.h +134 -0
  152. data/ext/bamtools/src/cmake_install.cmake +42 -0
  153. data/ext/bamtools/src/shared/bamtools_global.h +78 -0
  154. data/ext/bamtools/src/third_party/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
  155. data/ext/bamtools/src/third_party/CMakeFiles/progress.marks +1 -0
  156. data/ext/bamtools/src/third_party/CMakeLists.txt +10 -0
  157. data/ext/bamtools/src/third_party/Makefile +167 -0
  158. data/ext/bamtools/src/third_party/cmake_install.cmake +35 -0
  159. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
  160. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/CXX.includecache +144 -0
  161. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/DependInfo.cmake +27 -0
  162. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make +157 -0
  163. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/cmake_clean.cmake +13 -0
  164. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend.internal +31 -0
  165. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend.make +31 -0
  166. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/flags.make +8 -0
  167. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o +0 -0
  168. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o +0 -0
  169. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o +0 -0
  170. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/link.txt +1 -0
  171. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/progress.make +4 -0
  172. data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/progress.marks +1 -0
  173. data/ext/bamtools/src/third_party/jsoncpp/CMakeLists.txt +23 -0
  174. data/ext/bamtools/src/third_party/jsoncpp/LICENSE +55 -0
  175. data/ext/bamtools/src/third_party/jsoncpp/Makefile +263 -0
  176. data/ext/bamtools/src/third_party/jsoncpp/cmake_install.cmake +29 -0
  177. data/ext/bamtools/src/third_party/jsoncpp/json.h +15 -0
  178. data/ext/bamtools/src/third_party/jsoncpp/json_batchallocator.h +130 -0
  179. data/ext/bamtools/src/third_party/jsoncpp/json_config.h +42 -0
  180. data/ext/bamtools/src/third_party/jsoncpp/json_features.h +47 -0
  181. data/ext/bamtools/src/third_party/jsoncpp/json_forwards.h +42 -0
  182. data/ext/bamtools/src/third_party/jsoncpp/json_internalarray.inl +453 -0
  183. data/ext/bamtools/src/third_party/jsoncpp/json_internalmap.inl +612 -0
  184. data/ext/bamtools/src/third_party/jsoncpp/json_reader.cpp +870 -0
  185. data/ext/bamtools/src/third_party/jsoncpp/json_reader.h +201 -0
  186. data/ext/bamtools/src/third_party/jsoncpp/json_tool.h +93 -0
  187. data/ext/bamtools/src/third_party/jsoncpp/json_value.cpp +1701 -0
  188. data/ext/bamtools/src/third_party/jsoncpp/json_value.h +1059 -0
  189. data/ext/bamtools/src/third_party/jsoncpp/json_valueiterator.inl +297 -0
  190. data/ext/bamtools/src/third_party/jsoncpp/json_writer.cpp +819 -0
  191. data/ext/bamtools/src/third_party/jsoncpp/json_writer.h +179 -0
  192. data/ext/bamtools/src/toolkit/CMakeFiles/CMakeDirectoryInformation.cmake +25 -0
  193. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/CXX.includecache +698 -0
  194. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake +34 -0
  195. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o +0 -0
  196. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o +0 -0
  197. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o +0 -0
  198. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o +0 -0
  199. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o +0 -0
  200. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o +0 -0
  201. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o +0 -0
  202. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o +0 -0
  203. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o +0 -0
  204. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o +0 -0
  205. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o +0 -0
  206. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o +0 -0
  207. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o +0 -0
  208. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o +0 -0
  209. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make +447 -0
  210. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/cmake_clean.cmake +24 -0
  211. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/depend.internal +319 -0
  212. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/depend.make +319 -0
  213. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/flags.make +8 -0
  214. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/link.txt +1 -0
  215. data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/progress.make +15 -0
  216. data/ext/bamtools/src/toolkit/CMakeFiles/progress.marks +1 -0
  217. data/ext/bamtools/src/toolkit/CMakeLists.txt +44 -0
  218. data/ext/bamtools/src/toolkit/Makefile +560 -0
  219. data/ext/bamtools/src/toolkit/bamtools.cpp +163 -0
  220. data/ext/bamtools/src/toolkit/bamtools_convert.cpp +888 -0
  221. data/ext/bamtools/src/toolkit/bamtools_convert.h +37 -0
  222. data/ext/bamtools/src/toolkit/bamtools_count.cpp +187 -0
  223. data/ext/bamtools/src/toolkit/bamtools_count.h +37 -0
  224. data/ext/bamtools/src/toolkit/bamtools_coverage.cpp +196 -0
  225. data/ext/bamtools/src/toolkit/bamtools_coverage.h +37 -0
  226. data/ext/bamtools/src/toolkit/bamtools_filter.cpp +911 -0
  227. data/ext/bamtools/src/toolkit/bamtools_filter.h +37 -0
  228. data/ext/bamtools/src/toolkit/bamtools_header.cpp +122 -0
  229. data/ext/bamtools/src/toolkit/bamtools_header.h +38 -0
  230. data/ext/bamtools/src/toolkit/bamtools_index.cpp +126 -0
  231. data/ext/bamtools/src/toolkit/bamtools_index.h +37 -0
  232. data/ext/bamtools/src/toolkit/bamtools_merge.cpp +221 -0
  233. data/ext/bamtools/src/toolkit/bamtools_merge.h +37 -0
  234. data/ext/bamtools/src/toolkit/bamtools_random.cpp +255 -0
  235. data/ext/bamtools/src/toolkit/bamtools_random.h +37 -0
  236. data/ext/bamtools/src/toolkit/bamtools_resolve.cpp +1396 -0
  237. data/ext/bamtools/src/toolkit/bamtools_resolve.h +42 -0
  238. data/ext/bamtools/src/toolkit/bamtools_revert.cpp +194 -0
  239. data/ext/bamtools/src/toolkit/bamtools_revert.h +37 -0
  240. data/ext/bamtools/src/toolkit/bamtools_sort.cpp +410 -0
  241. data/ext/bamtools/src/toolkit/bamtools_sort.h +37 -0
  242. data/ext/bamtools/src/toolkit/bamtools_split.cpp +551 -0
  243. data/ext/bamtools/src/toolkit/bamtools_split.h +38 -0
  244. data/ext/bamtools/src/toolkit/bamtools_stats.cpp +286 -0
  245. data/ext/bamtools/src/toolkit/bamtools_stats.h +37 -0
  246. data/ext/bamtools/src/toolkit/bamtools_tool.h +35 -0
  247. data/ext/bamtools/src/toolkit/bamtools_version.h +20 -0
  248. data/ext/bamtools/src/toolkit/bamtools_version.h.in +20 -0
  249. data/ext/bamtools/src/toolkit/cmake_install.cmake +52 -0
  250. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/CXX.includecache +250 -0
  251. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake +29 -0
  252. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o +0 -0
  253. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o +0 -0
  254. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o +0 -0
  255. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o +0 -0
  256. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/build.make +184 -0
  257. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/cmake_clean.cmake +14 -0
  258. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/depend.internal +40 -0
  259. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/depend.make +40 -0
  260. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/flags.make +8 -0
  261. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/link.txt +1 -0
  262. data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/progress.make +5 -0
  263. data/ext/bamtools/src/utils/CMakeFiles/CMakeDirectoryInformation.cmake +23 -0
  264. data/ext/bamtools/src/utils/CMakeFiles/progress.marks +1 -0
  265. data/ext/bamtools/src/utils/CMakeLists.txt +30 -0
  266. data/ext/bamtools/src/utils/Makefile +290 -0
  267. data/ext/bamtools/src/utils/bamtools_fasta.cpp +632 -0
  268. data/ext/bamtools/src/utils/bamtools_fasta.h +47 -0
  269. data/ext/bamtools/src/utils/bamtools_filter_engine.h +552 -0
  270. data/ext/bamtools/src/utils/bamtools_filter_properties.h +195 -0
  271. data/ext/bamtools/src/utils/bamtools_filter_ruleparser.h +319 -0
  272. data/ext/bamtools/src/utils/bamtools_options.cpp +287 -0
  273. data/ext/bamtools/src/utils/bamtools_options.h +213 -0
  274. data/ext/bamtools/src/utils/bamtools_pileup_engine.cpp +327 -0
  275. data/ext/bamtools/src/utils/bamtools_pileup_engine.h +94 -0
  276. data/ext/bamtools/src/utils/bamtools_utilities.cpp +333 -0
  277. data/ext/bamtools/src/utils/bamtools_utilities.h +67 -0
  278. data/ext/bamtools/src/utils/bamtools_variant.h +128 -0
  279. data/ext/bamtools/src/utils/cmake_install.cmake +29 -0
  280. data/ext/bamtools/src/utils/utils_global.h +21 -0
  281. data/lib/ngs_server/version.rb +3 -0
  282. data/lib/ngs_server.rb +3 -0
  283. data/ngs_server.gemspec +23 -0
  284. metadata +339 -0
@@ -0,0 +1,290 @@
1
+ # CMAKE generated file: DO NOT EDIT!
2
+ # Generated by "Unix Makefiles" Generator, CMake Version 2.8
3
+
4
+ # Default target executed when no arguments are given to make.
5
+ default_target: all
6
+ .PHONY : default_target
7
+
8
+ #=============================================================================
9
+ # Special targets provided by cmake.
10
+
11
+ # Disable implicit rules so canoncical targets will work.
12
+ .SUFFIXES:
13
+
14
+ # Remove some rules from gmake that .SUFFIXES does not remove.
15
+ SUFFIXES =
16
+
17
+ .SUFFIXES: .hpux_make_needs_suffix_list
18
+
19
+ # Suppress display of executed commands.
20
+ $(VERBOSE).SILENT:
21
+
22
+ # A target that is always out of date.
23
+ cmake_force:
24
+ .PHONY : cmake_force
25
+
26
+ #=============================================================================
27
+ # Set environment variables for the build.
28
+
29
+ # The shell in which to execute make rules.
30
+ SHELL = /bin/sh
31
+
32
+ # The CMake executable.
33
+ CMAKE_COMMAND = /usr/local/Cellar/cmake/2.8.4/bin/cmake
34
+
35
+ # The command to remove a file.
36
+ RM = /usr/local/Cellar/cmake/2.8.4/bin/cmake -E remove -f
37
+
38
+ # The program to use to edit the cache.
39
+ CMAKE_EDIT_COMMAND = /usr/local/Cellar/cmake/2.8.4/bin/ccmake
40
+
41
+ # The top-level source directory on which CMake was run.
42
+ CMAKE_SOURCE_DIR = /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools
43
+
44
+ # The top-level build directory on which CMake was run.
45
+ CMAKE_BINARY_DIR = /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools
46
+
47
+ #=============================================================================
48
+ # Targets provided globally by CMake.
49
+
50
+ # Special rule for the target edit_cache
51
+ edit_cache:
52
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
53
+ /usr/local/Cellar/cmake/2.8.4/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
54
+ .PHONY : edit_cache
55
+
56
+ # Special rule for the target edit_cache
57
+ edit_cache/fast: edit_cache
58
+ .PHONY : edit_cache/fast
59
+
60
+ # Special rule for the target install
61
+ install: preinstall
62
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
63
+ /usr/local/Cellar/cmake/2.8.4/bin/cmake -P cmake_install.cmake
64
+ .PHONY : install
65
+
66
+ # Special rule for the target install
67
+ install/fast: preinstall/fast
68
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
69
+ /usr/local/Cellar/cmake/2.8.4/bin/cmake -P cmake_install.cmake
70
+ .PHONY : install/fast
71
+
72
+ # Special rule for the target install/local
73
+ install/local: preinstall
74
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
75
+ /usr/local/Cellar/cmake/2.8.4/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
76
+ .PHONY : install/local
77
+
78
+ # Special rule for the target install/local
79
+ install/local/fast: install/local
80
+ .PHONY : install/local/fast
81
+
82
+ # Special rule for the target install/strip
83
+ install/strip: preinstall
84
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
85
+ /usr/local/Cellar/cmake/2.8.4/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
86
+ .PHONY : install/strip
87
+
88
+ # Special rule for the target install/strip
89
+ install/strip/fast: install/strip
90
+ .PHONY : install/strip/fast
91
+
92
+ # Special rule for the target list_install_components
93
+ list_install_components:
94
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
95
+ .PHONY : list_install_components
96
+
97
+ # Special rule for the target list_install_components
98
+ list_install_components/fast: list_install_components
99
+ .PHONY : list_install_components/fast
100
+
101
+ # Special rule for the target rebuild_cache
102
+ rebuild_cache:
103
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake to regenerate build system..."
104
+ /usr/local/Cellar/cmake/2.8.4/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
105
+ .PHONY : rebuild_cache
106
+
107
+ # Special rule for the target rebuild_cache
108
+ rebuild_cache/fast: rebuild_cache
109
+ .PHONY : rebuild_cache/fast
110
+
111
+ # The main all target
112
+ all: cmake_check_build_system
113
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -E cmake_progress_start /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/CMakeFiles /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/utils/CMakeFiles/progress.marks
114
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/utils/all
115
+ $(CMAKE_COMMAND) -E cmake_progress_start /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/CMakeFiles 0
116
+ .PHONY : all
117
+
118
+ # The main clean target
119
+ clean:
120
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/utils/clean
121
+ .PHONY : clean
122
+
123
+ # The main clean target
124
+ clean/fast: clean
125
+ .PHONY : clean/fast
126
+
127
+ # Prepare targets for installation.
128
+ preinstall: all
129
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/utils/preinstall
130
+ .PHONY : preinstall
131
+
132
+ # Prepare targets for installation.
133
+ preinstall/fast:
134
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/utils/preinstall
135
+ .PHONY : preinstall/fast
136
+
137
+ # clear depends
138
+ depend:
139
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
140
+ .PHONY : depend
141
+
142
+ # Convenience name for target.
143
+ src/utils/CMakeFiles/BamTools-utils.dir/rule:
144
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/utils/CMakeFiles/BamTools-utils.dir/rule
145
+ .PHONY : src/utils/CMakeFiles/BamTools-utils.dir/rule
146
+
147
+ # Convenience name for target.
148
+ BamTools-utils: src/utils/CMakeFiles/BamTools-utils.dir/rule
149
+ .PHONY : BamTools-utils
150
+
151
+ # fast build rule for target.
152
+ BamTools-utils/fast:
153
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build
154
+ .PHONY : BamTools-utils/fast
155
+
156
+ bamtools_fasta.o: bamtools_fasta.cpp.o
157
+ .PHONY : bamtools_fasta.o
158
+
159
+ # target to build an object file
160
+ bamtools_fasta.cpp.o:
161
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
162
+ .PHONY : bamtools_fasta.cpp.o
163
+
164
+ bamtools_fasta.i: bamtools_fasta.cpp.i
165
+ .PHONY : bamtools_fasta.i
166
+
167
+ # target to preprocess a source file
168
+ bamtools_fasta.cpp.i:
169
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.i
170
+ .PHONY : bamtools_fasta.cpp.i
171
+
172
+ bamtools_fasta.s: bamtools_fasta.cpp.s
173
+ .PHONY : bamtools_fasta.s
174
+
175
+ # target to generate assembly for a file
176
+ bamtools_fasta.cpp.s:
177
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.s
178
+ .PHONY : bamtools_fasta.cpp.s
179
+
180
+ bamtools_options.o: bamtools_options.cpp.o
181
+ .PHONY : bamtools_options.o
182
+
183
+ # target to build an object file
184
+ bamtools_options.cpp.o:
185
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
186
+ .PHONY : bamtools_options.cpp.o
187
+
188
+ bamtools_options.i: bamtools_options.cpp.i
189
+ .PHONY : bamtools_options.i
190
+
191
+ # target to preprocess a source file
192
+ bamtools_options.cpp.i:
193
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.i
194
+ .PHONY : bamtools_options.cpp.i
195
+
196
+ bamtools_options.s: bamtools_options.cpp.s
197
+ .PHONY : bamtools_options.s
198
+
199
+ # target to generate assembly for a file
200
+ bamtools_options.cpp.s:
201
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.s
202
+ .PHONY : bamtools_options.cpp.s
203
+
204
+ bamtools_pileup_engine.o: bamtools_pileup_engine.cpp.o
205
+ .PHONY : bamtools_pileup_engine.o
206
+
207
+ # target to build an object file
208
+ bamtools_pileup_engine.cpp.o:
209
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
210
+ .PHONY : bamtools_pileup_engine.cpp.o
211
+
212
+ bamtools_pileup_engine.i: bamtools_pileup_engine.cpp.i
213
+ .PHONY : bamtools_pileup_engine.i
214
+
215
+ # target to preprocess a source file
216
+ bamtools_pileup_engine.cpp.i:
217
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.i
218
+ .PHONY : bamtools_pileup_engine.cpp.i
219
+
220
+ bamtools_pileup_engine.s: bamtools_pileup_engine.cpp.s
221
+ .PHONY : bamtools_pileup_engine.s
222
+
223
+ # target to generate assembly for a file
224
+ bamtools_pileup_engine.cpp.s:
225
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.s
226
+ .PHONY : bamtools_pileup_engine.cpp.s
227
+
228
+ bamtools_utilities.o: bamtools_utilities.cpp.o
229
+ .PHONY : bamtools_utilities.o
230
+
231
+ # target to build an object file
232
+ bamtools_utilities.cpp.o:
233
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
234
+ .PHONY : bamtools_utilities.cpp.o
235
+
236
+ bamtools_utilities.i: bamtools_utilities.cpp.i
237
+ .PHONY : bamtools_utilities.i
238
+
239
+ # target to preprocess a source file
240
+ bamtools_utilities.cpp.i:
241
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.i
242
+ .PHONY : bamtools_utilities.cpp.i
243
+
244
+ bamtools_utilities.s: bamtools_utilities.cpp.s
245
+ .PHONY : bamtools_utilities.s
246
+
247
+ # target to generate assembly for a file
248
+ bamtools_utilities.cpp.s:
249
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.s
250
+ .PHONY : bamtools_utilities.cpp.s
251
+
252
+ # Help Target
253
+ help:
254
+ @echo "The following are some of the valid targets for this Makefile:"
255
+ @echo "... all (the default if no target is provided)"
256
+ @echo "... clean"
257
+ @echo "... depend"
258
+ @echo "... BamTools-utils"
259
+ @echo "... edit_cache"
260
+ @echo "... install"
261
+ @echo "... install/local"
262
+ @echo "... install/strip"
263
+ @echo "... list_install_components"
264
+ @echo "... rebuild_cache"
265
+ @echo "... bamtools_fasta.o"
266
+ @echo "... bamtools_fasta.i"
267
+ @echo "... bamtools_fasta.s"
268
+ @echo "... bamtools_options.o"
269
+ @echo "... bamtools_options.i"
270
+ @echo "... bamtools_options.s"
271
+ @echo "... bamtools_pileup_engine.o"
272
+ @echo "... bamtools_pileup_engine.i"
273
+ @echo "... bamtools_pileup_engine.s"
274
+ @echo "... bamtools_utilities.o"
275
+ @echo "... bamtools_utilities.i"
276
+ @echo "... bamtools_utilities.s"
277
+ .PHONY : help
278
+
279
+
280
+
281
+ #=============================================================================
282
+ # Special targets to cleanup operation of make.
283
+
284
+ # Special rule to run CMake to check the build system integrity.
285
+ # No rule that depends on this can have commands that come from listfiles
286
+ # because they might be regenerated.
287
+ cmake_check_build_system:
288
+ cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
289
+ .PHONY : cmake_check_build_system
290
+