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 +1,47 @@
1
+ # The set of languages for which implicit dependencies are needed:
2
+ SET(CMAKE_DEPENDS_LANGUAGES
3
+ "CXX"
4
+ )
5
+ # The set of files for implicit dependencies of each language:
6
+ SET(CMAKE_DEPENDS_CHECK_CXX
7
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamAlignment.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o"
8
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamMultiReader.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o"
9
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamReader.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o"
10
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamWriter.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o"
11
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamHeader.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o"
12
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamProgram.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o"
13
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamProgramChain.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o"
14
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamReadGroup.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o"
15
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamReadGroupDictionary.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o"
16
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamSequence.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o"
17
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamSequenceDictionary.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o"
18
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamHeader_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamHeader_p.cpp.o"
19
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamIndexFactory_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamIndexFactory_p.cpp.o"
20
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamMultiReader_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamMultiReader_p.cpp.o"
21
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamRandomAccessController_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamRandomAccessController_p.cpp.o"
22
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamReader_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamReader_p.cpp.o"
23
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamStandardIndex_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamStandardIndex_p.cpp.o"
24
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamToolsIndex_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamToolsIndex_p.cpp.o"
25
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BamWriter_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamWriter_p.cpp.o"
26
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/BgzfStream_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BgzfStream_p.cpp.o"
27
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/SamFormatParser_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamFormatParser_p.cpp.o"
28
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/SamFormatPrinter_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamFormatPrinter_p.cpp.o"
29
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/internal/SamHeaderValidator_p.cpp" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamHeaderValidator_p.cpp.o"
30
+ )
31
+ SET(CMAKE_CXX_COMPILER_ID "GNU")
32
+
33
+ # Preprocessor definitions for this target.
34
+ SET(CMAKE_TARGET_DEFINITIONS
35
+ "_FILE_OFFSET_BITS=64"
36
+ "BAMTOOLS_API_LIBRARY"
37
+ )
38
+
39
+ # Pairs of files generated by the same build rule.
40
+ SET(CMAKE_MULTIPLE_OUTPUT_PAIRS
41
+ "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/lib/libbamtools.dylib" "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/lib/libbamtools.1.0.2.dylib"
42
+ )
43
+
44
+
45
+ # Targets to which this target links.
46
+ SET(CMAKE_TARGET_LINKED_INFO_FILES
47
+ )