ngs_server 0.1

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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
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  27. data/ext/bamtools/src/api/BamIndex.h +79 -0
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+ jurisdictions which recognize such a disclaimer. In such jurisdictions,
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+ this software is released into the Public Domain.
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+
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+ In jurisdictions which do not recognize Public Domain property (e.g. Germany as of
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+ 2010), this software is Copyright (c) 2007-2010 by Baptiste Lepilleur, and is
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+ released under the terms of the MIT License (see below).
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+
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+ In jurisdictions which recognize Public Domain property, the user of this
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+
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+ http://en.wikipedia.org/wiki/MIT_License
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+
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+ The full text of the MIT License follows:
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+
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+ ========================================================================
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+ Copyright (c) 2007-2010 Baptiste Lepilleur
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+
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+ Permission is hereby granted, free of charge, to any person
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+ obtaining a copy of this software and associated documentation
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+ files (the "Software"), to deal in the Software without
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+ The above copyright notice and this permission notice shall be
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
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+ ========================================================================
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+ (END LICENSE TEXT)
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+ The MIT license is compatible with both the GPL and commercial
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+ minor nuisance of being required to keep the above copyright notice
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+ and license text in the source code. Note also that by accepting the
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+ # Special rule to run CMake to check the build system integrity.
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+ # No rule that depends on this can have commands that come from listfiles
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+ # because they might be regenerated.
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+ cmake_check_build_system:
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+ 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
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+ .PHONY : cmake_check_build_system
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+