ngs_server 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.
- data/.gitignore +4 -0
- data/Gemfile +4 -0
- data/Rakefile +2 -0
- data/bin/ngs_server +58 -0
- data/data/holder.txt +0 -0
- data/ext/bamtools/CMakeLists.txt +49 -0
- data/ext/bamtools/LICENSE +22 -0
- data/ext/bamtools/README +60 -0
- data/ext/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf +0 -0
- data/ext/bamtools/docs/Doxyfile +1601 -0
- data/ext/bamtools/extconf.rb +9 -0
- data/ext/bamtools/src/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
- data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake +13 -0
- data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/build.make +65 -0
- data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/cmake_clean.cmake +8 -0
- data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/depend.internal +3 -0
- data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/depend.make +3 -0
- data/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/progress.make +2 -0
- data/ext/bamtools/src/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/CMakeLists.txt +18 -0
- data/ext/bamtools/src/ExportHeader.cmake +31 -0
- data/ext/bamtools/src/Makefile +182 -0
- data/ext/bamtools/src/api/BamAlignment.cpp +2432 -0
- data/ext/bamtools/src/api/BamAlignment.h +206 -0
- data/ext/bamtools/src/api/BamAux.h +456 -0
- data/ext/bamtools/src/api/BamConstants.h +127 -0
- data/ext/bamtools/src/api/BamIndex.h +79 -0
- data/ext/bamtools/src/api/BamMultiReader.cpp +395 -0
- data/ext/bamtools/src/api/BamMultiReader.h +126 -0
- data/ext/bamtools/src/api/BamReader.cpp +369 -0
- data/ext/bamtools/src/api/BamReader.h +117 -0
- data/ext/bamtools/src/api/BamWriter.cpp +142 -0
- data/ext/bamtools/src/api/BamWriter.h +63 -0
- data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake +14 -0
- data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/build.make +80 -0
- data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/cmake_clean.cmake +8 -0
- data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/depend.internal +3 -0
- data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/depend.make +3 -0
- data/ext/bamtools/src/api/CMakeFiles/APIHeaders.dir/progress.make +2 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/CXX.includecache +596 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/DependInfo.cmake +41 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/build.make +675 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/cmake_clean.cmake +32 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/cmake_clean_target.cmake +3 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/depend.internal +295 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/depend.make +295 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/flags.make +8 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamHeader_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamIndexFactory_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamMultiReader_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamRandomAccessController_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamReader_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamStandardIndex_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamToolsIndex_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BamWriter_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/BgzfStream_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/SamFormatParser_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/SamFormatPrinter_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/internal/SamHeaderValidator_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/link.txt +2 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools-static.dir/progress.make +24 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/CXX.includecache +596 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake +47 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/build.make +677 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/cmake_clean.cmake +33 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/depend.internal +295 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/depend.make +295 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/flags.make +8 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamHeader_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamIndexFactory_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamMultiReader_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamRandomAccessController_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamReader_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamStandardIndex_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamToolsIndex_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BamWriter_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/BgzfStream_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamFormatParser_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamFormatPrinter_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/internal/SamHeaderValidator_p.cpp.o +0 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/link.txt +1 -0
- data/ext/bamtools/src/api/CMakeFiles/BamTools.dir/progress.make +24 -0
- data/ext/bamtools/src/api/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
- data/ext/bamtools/src/api/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/api/CMakeLists.txt +78 -0
- data/ext/bamtools/src/api/Makefile +902 -0
- data/ext/bamtools/src/api/SamConstants.h +95 -0
- data/ext/bamtools/src/api/SamHeader.cpp +184 -0
- data/ext/bamtools/src/api/SamHeader.h +68 -0
- data/ext/bamtools/src/api/SamProgram.cpp +139 -0
- data/ext/bamtools/src/api/SamProgram.h +61 -0
- data/ext/bamtools/src/api/SamProgramChain.cpp +351 -0
- data/ext/bamtools/src/api/SamProgramChain.h +85 -0
- data/ext/bamtools/src/api/SamReadGroup.cpp +221 -0
- data/ext/bamtools/src/api/SamReadGroup.h +68 -0
- data/ext/bamtools/src/api/SamReadGroupDictionary.cpp +289 -0
- data/ext/bamtools/src/api/SamReadGroupDictionary.h +86 -0
- data/ext/bamtools/src/api/SamSequence.cpp +161 -0
- data/ext/bamtools/src/api/SamSequence.h +60 -0
- data/ext/bamtools/src/api/SamSequenceDictionary.cpp +292 -0
- data/ext/bamtools/src/api/SamSequenceDictionary.h +88 -0
- data/ext/bamtools/src/api/api_global.h +21 -0
- data/ext/bamtools/src/api/cmake_install.cmake +122 -0
- data/ext/bamtools/src/api/internal/BamHeader_p.cpp +132 -0
- data/ext/bamtools/src/api/internal/BamHeader_p.h +71 -0
- data/ext/bamtools/src/api/internal/BamIndexFactory_p.cpp +112 -0
- data/ext/bamtools/src/api/internal/BamIndexFactory_p.h +49 -0
- data/ext/bamtools/src/api/internal/BamMultiMerger_p.h +297 -0
- data/ext/bamtools/src/api/internal/BamMultiReader_p.cpp +805 -0
- data/ext/bamtools/src/api/internal/BamMultiReader_p.h +103 -0
- data/ext/bamtools/src/api/internal/BamRandomAccessController_p.cpp +272 -0
- data/ext/bamtools/src/api/internal/BamRandomAccessController_p.h +93 -0
- data/ext/bamtools/src/api/internal/BamReader_p.cpp +380 -0
- data/ext/bamtools/src/api/internal/BamReader_p.h +112 -0
- data/ext/bamtools/src/api/internal/BamStandardIndex_p.cpp +986 -0
- data/ext/bamtools/src/api/internal/BamStandardIndex_p.h +236 -0
- data/ext/bamtools/src/api/internal/BamToolsIndex_p.cpp +641 -0
- data/ext/bamtools/src/api/internal/BamToolsIndex_p.h +187 -0
- data/ext/bamtools/src/api/internal/BamWriter_p.cpp +424 -0
- data/ext/bamtools/src/api/internal/BamWriter_p.h +66 -0
- data/ext/bamtools/src/api/internal/BgzfStream_p.cpp +438 -0
- data/ext/bamtools/src/api/internal/BgzfStream_p.h +108 -0
- data/ext/bamtools/src/api/internal/SamFormatParser_p.cpp +230 -0
- data/ext/bamtools/src/api/internal/SamFormatParser_p.h +61 -0
- data/ext/bamtools/src/api/internal/SamFormatPrinter_p.cpp +210 -0
- data/ext/bamtools/src/api/internal/SamFormatPrinter_p.h +60 -0
- data/ext/bamtools/src/api/internal/SamHeaderValidator_p.cpp +510 -0
- data/ext/bamtools/src/api/internal/SamHeaderValidator_p.h +101 -0
- data/ext/bamtools/src/api/internal/SamHeaderVersion_p.h +134 -0
- data/ext/bamtools/src/cmake_install.cmake +42 -0
- data/ext/bamtools/src/shared/bamtools_global.h +78 -0
- data/ext/bamtools/src/third_party/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
- data/ext/bamtools/src/third_party/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/third_party/CMakeLists.txt +10 -0
- data/ext/bamtools/src/third_party/Makefile +167 -0
- data/ext/bamtools/src/third_party/cmake_install.cmake +35 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/CMakeDirectoryInformation.cmake +22 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/CXX.includecache +144 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/DependInfo.cmake +27 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make +157 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/cmake_clean.cmake +13 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend.internal +31 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend.make +31 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/flags.make +8 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o +0 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o +0 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o +0 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/link.txt +1 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/progress.make +4 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/third_party/jsoncpp/CMakeLists.txt +23 -0
- data/ext/bamtools/src/third_party/jsoncpp/LICENSE +55 -0
- data/ext/bamtools/src/third_party/jsoncpp/Makefile +263 -0
- data/ext/bamtools/src/third_party/jsoncpp/cmake_install.cmake +29 -0
- data/ext/bamtools/src/third_party/jsoncpp/json.h +15 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_batchallocator.h +130 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_config.h +42 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_features.h +47 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_forwards.h +42 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_internalarray.inl +453 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_internalmap.inl +612 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_reader.cpp +870 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_reader.h +201 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_tool.h +93 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_value.cpp +1701 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_value.h +1059 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_valueiterator.inl +297 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_writer.cpp +819 -0
- data/ext/bamtools/src/third_party/jsoncpp/json_writer.h +179 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/CMakeDirectoryInformation.cmake +25 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/CXX.includecache +698 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake +34 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o +0 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make +447 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/cmake_clean.cmake +24 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/depend.internal +319 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/depend.make +319 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/flags.make +8 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/link.txt +1 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/bamtools_cmd.dir/progress.make +15 -0
- data/ext/bamtools/src/toolkit/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/toolkit/CMakeLists.txt +44 -0
- data/ext/bamtools/src/toolkit/Makefile +560 -0
- data/ext/bamtools/src/toolkit/bamtools.cpp +163 -0
- data/ext/bamtools/src/toolkit/bamtools_convert.cpp +888 -0
- data/ext/bamtools/src/toolkit/bamtools_convert.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_count.cpp +187 -0
- data/ext/bamtools/src/toolkit/bamtools_count.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_coverage.cpp +196 -0
- data/ext/bamtools/src/toolkit/bamtools_coverage.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_filter.cpp +911 -0
- data/ext/bamtools/src/toolkit/bamtools_filter.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_header.cpp +122 -0
- data/ext/bamtools/src/toolkit/bamtools_header.h +38 -0
- data/ext/bamtools/src/toolkit/bamtools_index.cpp +126 -0
- data/ext/bamtools/src/toolkit/bamtools_index.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_merge.cpp +221 -0
- data/ext/bamtools/src/toolkit/bamtools_merge.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_random.cpp +255 -0
- data/ext/bamtools/src/toolkit/bamtools_random.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_resolve.cpp +1396 -0
- data/ext/bamtools/src/toolkit/bamtools_resolve.h +42 -0
- data/ext/bamtools/src/toolkit/bamtools_revert.cpp +194 -0
- data/ext/bamtools/src/toolkit/bamtools_revert.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_sort.cpp +410 -0
- data/ext/bamtools/src/toolkit/bamtools_sort.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_split.cpp +551 -0
- data/ext/bamtools/src/toolkit/bamtools_split.h +38 -0
- data/ext/bamtools/src/toolkit/bamtools_stats.cpp +286 -0
- data/ext/bamtools/src/toolkit/bamtools_stats.h +37 -0
- data/ext/bamtools/src/toolkit/bamtools_tool.h +35 -0
- data/ext/bamtools/src/toolkit/bamtools_version.h +20 -0
- data/ext/bamtools/src/toolkit/bamtools_version.h.in +20 -0
- data/ext/bamtools/src/toolkit/cmake_install.cmake +52 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/CXX.includecache +250 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake +29 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o +0 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o +0 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o +0 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o +0 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/build.make +184 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/cmake_clean.cmake +14 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/depend.internal +40 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/depend.make +40 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/flags.make +8 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/link.txt +1 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/progress.make +5 -0
- data/ext/bamtools/src/utils/CMakeFiles/CMakeDirectoryInformation.cmake +23 -0
- data/ext/bamtools/src/utils/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/utils/CMakeLists.txt +30 -0
- data/ext/bamtools/src/utils/Makefile +290 -0
- data/ext/bamtools/src/utils/bamtools_fasta.cpp +632 -0
- data/ext/bamtools/src/utils/bamtools_fasta.h +47 -0
- data/ext/bamtools/src/utils/bamtools_filter_engine.h +552 -0
- data/ext/bamtools/src/utils/bamtools_filter_properties.h +195 -0
- data/ext/bamtools/src/utils/bamtools_filter_ruleparser.h +319 -0
- data/ext/bamtools/src/utils/bamtools_options.cpp +287 -0
- data/ext/bamtools/src/utils/bamtools_options.h +213 -0
- data/ext/bamtools/src/utils/bamtools_pileup_engine.cpp +327 -0
- data/ext/bamtools/src/utils/bamtools_pileup_engine.h +94 -0
- data/ext/bamtools/src/utils/bamtools_utilities.cpp +333 -0
- data/ext/bamtools/src/utils/bamtools_utilities.h +67 -0
- data/ext/bamtools/src/utils/bamtools_variant.h +128 -0
- data/ext/bamtools/src/utils/cmake_install.cmake +29 -0
- data/ext/bamtools/src/utils/utils_global.h +21 -0
- data/lib/ngs_server/version.rb +3 -0
- data/lib/ngs_server.rb +3 -0
- data/ngs_server.gemspec +23 -0
- metadata +339 -0
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
# CMAKE generated file: DO NOT EDIT!
|
|
2
|
+
# Generated by "Unix Makefiles" Generator, CMake Version 2.8
|
|
3
|
+
|
|
4
|
+
# Relative path conversion top directories.
|
|
5
|
+
SET(CMAKE_RELATIVE_PATH_TOP_SOURCE "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
|
|
6
|
+
SET(CMAKE_RELATIVE_PATH_TOP_BINARY "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
|
|
7
|
+
|
|
8
|
+
# Force unix paths in dependencies.
|
|
9
|
+
SET(CMAKE_FORCE_UNIX_PATHS 1)
|
|
10
|
+
|
|
11
|
+
# The C and CXX include file search paths:
|
|
12
|
+
SET(CMAKE_C_INCLUDE_PATH
|
|
13
|
+
"src"
|
|
14
|
+
)
|
|
15
|
+
SET(CMAKE_CXX_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
|
|
16
|
+
SET(CMAKE_Fortran_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
|
|
17
|
+
|
|
18
|
+
# The C and CXX include file regular expressions for this directory.
|
|
19
|
+
SET(CMAKE_C_INCLUDE_REGEX_SCAN "^.*$")
|
|
20
|
+
SET(CMAKE_C_INCLUDE_REGEX_COMPLAIN "^$")
|
|
21
|
+
SET(CMAKE_CXX_INCLUDE_REGEX_SCAN ${CMAKE_C_INCLUDE_REGEX_SCAN})
|
|
22
|
+
SET(CMAKE_CXX_INCLUDE_REGEX_COMPLAIN ${CMAKE_C_INCLUDE_REGEX_COMPLAIN})
|
|
@@ -0,0 +1,13 @@
|
|
|
1
|
+
# The set of languages for which implicit dependencies are needed:
|
|
2
|
+
SET(CMAKE_DEPENDS_LANGUAGES
|
|
3
|
+
)
|
|
4
|
+
# The set of files for implicit dependencies of each language:
|
|
5
|
+
|
|
6
|
+
# Preprocessor definitions for this target.
|
|
7
|
+
SET(CMAKE_TARGET_DEFINITIONS
|
|
8
|
+
"_FILE_OFFSET_BITS=64"
|
|
9
|
+
)
|
|
10
|
+
|
|
11
|
+
# Targets to which this target links.
|
|
12
|
+
SET(CMAKE_TARGET_LINKED_INFO_FILES
|
|
13
|
+
)
|
|
@@ -0,0 +1,65 @@
|
|
|
1
|
+
# CMAKE generated file: DO NOT EDIT!
|
|
2
|
+
# Generated by "Unix Makefiles" Generator, CMake Version 2.8
|
|
3
|
+
|
|
4
|
+
#=============================================================================
|
|
5
|
+
# Special targets provided by cmake.
|
|
6
|
+
|
|
7
|
+
# Disable implicit rules so canoncical targets will work.
|
|
8
|
+
.SUFFIXES:
|
|
9
|
+
|
|
10
|
+
# Remove some rules from gmake that .SUFFIXES does not remove.
|
|
11
|
+
SUFFIXES =
|
|
12
|
+
|
|
13
|
+
.SUFFIXES: .hpux_make_needs_suffix_list
|
|
14
|
+
|
|
15
|
+
# Suppress display of executed commands.
|
|
16
|
+
$(VERBOSE).SILENT:
|
|
17
|
+
|
|
18
|
+
# A target that is always out of date.
|
|
19
|
+
cmake_force:
|
|
20
|
+
.PHONY : cmake_force
|
|
21
|
+
|
|
22
|
+
#=============================================================================
|
|
23
|
+
# Set environment variables for the build.
|
|
24
|
+
|
|
25
|
+
# The shell in which to execute make rules.
|
|
26
|
+
SHELL = /bin/sh
|
|
27
|
+
|
|
28
|
+
# The CMake executable.
|
|
29
|
+
CMAKE_COMMAND = /usr/local/Cellar/cmake/2.8.4/bin/cmake
|
|
30
|
+
|
|
31
|
+
# The command to remove a file.
|
|
32
|
+
RM = /usr/local/Cellar/cmake/2.8.4/bin/cmake -E remove -f
|
|
33
|
+
|
|
34
|
+
# The program to use to edit the cache.
|
|
35
|
+
CMAKE_EDIT_COMMAND = /usr/local/Cellar/cmake/2.8.4/bin/ccmake
|
|
36
|
+
|
|
37
|
+
# The top-level source directory on which CMake was run.
|
|
38
|
+
CMAKE_SOURCE_DIR = /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools
|
|
39
|
+
|
|
40
|
+
# The top-level build directory on which CMake was run.
|
|
41
|
+
CMAKE_BINARY_DIR = /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools
|
|
42
|
+
|
|
43
|
+
# Utility rule file for SharedHeaders.
|
|
44
|
+
|
|
45
|
+
src/CMakeFiles/SharedHeaders:
|
|
46
|
+
$(CMAKE_COMMAND) -E cmake_progress_report /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/CMakeFiles $(CMAKE_PROGRESS_1)
|
|
47
|
+
@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --blue --bold "Exporting SharedHeaders"
|
|
48
|
+
|
|
49
|
+
SharedHeaders: src/CMakeFiles/SharedHeaders
|
|
50
|
+
SharedHeaders: src/CMakeFiles/SharedHeaders.dir/build.make
|
|
51
|
+
cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src && /usr/local/Cellar/cmake/2.8.4/bin/cmake -E copy_if_different /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/shared/bamtools_global.h /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/include/shared/bamtools_global.h
|
|
52
|
+
.PHONY : SharedHeaders
|
|
53
|
+
|
|
54
|
+
# Rule to build all files generated by this target.
|
|
55
|
+
src/CMakeFiles/SharedHeaders.dir/build: SharedHeaders
|
|
56
|
+
.PHONY : src/CMakeFiles/SharedHeaders.dir/build
|
|
57
|
+
|
|
58
|
+
src/CMakeFiles/SharedHeaders.dir/clean:
|
|
59
|
+
cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src && $(CMAKE_COMMAND) -P CMakeFiles/SharedHeaders.dir/cmake_clean.cmake
|
|
60
|
+
.PHONY : src/CMakeFiles/SharedHeaders.dir/clean
|
|
61
|
+
|
|
62
|
+
src/CMakeFiles/SharedHeaders.dir/depend:
|
|
63
|
+
cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -E cmake_depends "Unix Makefiles" /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake --color=$(COLOR)
|
|
64
|
+
.PHONY : src/CMakeFiles/SharedHeaders.dir/depend
|
|
65
|
+
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
69
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
# ==========================
|
|
2
|
+
# BamTools CMakeLists.txt
|
|
3
|
+
# (c) 2010 Derek Barnett
|
|
4
|
+
#
|
|
5
|
+
# src/
|
|
6
|
+
# ==========================
|
|
7
|
+
|
|
8
|
+
add_subdirectory (api)
|
|
9
|
+
add_subdirectory (utils)
|
|
10
|
+
add_subdirectory (third_party)
|
|
11
|
+
add_subdirectory (toolkit)
|
|
12
|
+
|
|
13
|
+
# export shared headers
|
|
14
|
+
include(ExportHeader.cmake)
|
|
15
|
+
set(SharedIncludeDir "shared")
|
|
16
|
+
ExportHeader(SharedHeaders shared/bamtools_global.h ${SharedIncludeDir})
|
|
17
|
+
|
|
18
|
+
|
|
@@ -0,0 +1,31 @@
|
|
|
1
|
+
#
|
|
2
|
+
# ExportHeader
|
|
3
|
+
#
|
|
4
|
+
|
|
5
|
+
function( ExportHeader MODULE FILE DEST )
|
|
6
|
+
|
|
7
|
+
# if haven't defined our custom 'build target'
|
|
8
|
+
# not exactly a build target, but lets this command get
|
|
9
|
+
# checked any time build step happens
|
|
10
|
+
if (NOT TARGET ${MODULE})
|
|
11
|
+
add_custom_target( ${MODULE} ALL COMMENT "Exporting ${MODULE}" )
|
|
12
|
+
endif (NOT TARGET ${MODULE} )
|
|
13
|
+
|
|
14
|
+
# get the filename (without path)
|
|
15
|
+
get_filename_component( FILENAME "${FILE}" NAME )
|
|
16
|
+
|
|
17
|
+
# copy header to destination
|
|
18
|
+
add_custom_command( TARGET ${MODULE} COMMAND
|
|
19
|
+
${CMAKE_COMMAND} -E copy_if_different
|
|
20
|
+
"${CMAKE_CURRENT_SOURCE_DIR}/${FILE}"
|
|
21
|
+
"${CMAKE_SOURCE_DIR}/include/${DEST}/${FILENAME}" )
|
|
22
|
+
|
|
23
|
+
|
|
24
|
+
|
|
25
|
+
# make sure files are properly 'installed'
|
|
26
|
+
# set(INSTALL_DEST "bamtools/${DEST}")
|
|
27
|
+
# install( FILES "${FILE}" DESTINATION "${INSTALL_DEST}")
|
|
28
|
+
install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" )
|
|
29
|
+
|
|
30
|
+
endfunction( ExportHeader )
|
|
31
|
+
|
|
@@ -0,0 +1,182 @@
|
|
|
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/CMakeFiles/progress.marks
|
|
114
|
+
cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/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/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/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/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/CMakeFiles/SharedHeaders.dir/rule:
|
|
144
|
+
cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/CMakeFiles/SharedHeaders.dir/rule
|
|
145
|
+
.PHONY : src/CMakeFiles/SharedHeaders.dir/rule
|
|
146
|
+
|
|
147
|
+
# Convenience name for target.
|
|
148
|
+
SharedHeaders: src/CMakeFiles/SharedHeaders.dir/rule
|
|
149
|
+
.PHONY : SharedHeaders
|
|
150
|
+
|
|
151
|
+
# fast build rule for target.
|
|
152
|
+
SharedHeaders/fast:
|
|
153
|
+
cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/build
|
|
154
|
+
.PHONY : SharedHeaders/fast
|
|
155
|
+
|
|
156
|
+
# Help Target
|
|
157
|
+
help:
|
|
158
|
+
@echo "The following are some of the valid targets for this Makefile:"
|
|
159
|
+
@echo "... all (the default if no target is provided)"
|
|
160
|
+
@echo "... clean"
|
|
161
|
+
@echo "... depend"
|
|
162
|
+
@echo "... SharedHeaders"
|
|
163
|
+
@echo "... edit_cache"
|
|
164
|
+
@echo "... install"
|
|
165
|
+
@echo "... install/local"
|
|
166
|
+
@echo "... install/strip"
|
|
167
|
+
@echo "... list_install_components"
|
|
168
|
+
@echo "... rebuild_cache"
|
|
169
|
+
.PHONY : help
|
|
170
|
+
|
|
171
|
+
|
|
172
|
+
|
|
173
|
+
#=============================================================================
|
|
174
|
+
# Special targets to cleanup operation of make.
|
|
175
|
+
|
|
176
|
+
# Special rule to run CMake to check the build system integrity.
|
|
177
|
+
# No rule that depends on this can have commands that come from listfiles
|
|
178
|
+
# because they might be regenerated.
|
|
179
|
+
cmake_check_build_system:
|
|
180
|
+
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
|
|
181
|
+
.PHONY : cmake_check_build_system
|
|
182
|
+
|