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README : BAMTOOLS
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BamTools provides both a programmer's API and an end-user's toolkit for handling
BAM files.

I.   Learn More

II.  License

III. Acknowledgements

IV.  Contact

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I. Learn More:
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Installation steps, tutorial, API documentation, etc. are all now available 
through the BamTools project wiki:

https://github.com/pezmaster31/bamtools/wiki

Join the mailing list(s) to stay informed of updates or get involved with 
contributing:

https://github.com/pezmaster31/bamtools/wiki/Mailing-lists

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II. License :
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Both the BamTools API and toolkit are released under the MIT License.
Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
    Michael Stromberg

See included file LICENSE for details.

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III. Acknowledgements :
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 * Aaron Quinlan for several key feature ideas and bug fix contributions
 * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
 * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.

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IV. Contact :
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Feel free to contact me with any questions, comments, suggestions, bug reports,
    etc.

Derek Barnett
Marth Lab
Biology Dept., Boston College

Email: derekwbarnett@gmail.com
Project Website: http://github.com/pezmaster31/bamtools

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Different build types
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mkdir Release
cd Release
cmake -DCMAKE_BUILD_TYPE=Release ..
make

And for Debug (again from the root of your project):

mkdir Debug
cd Debug
cmake -DCMAKE_BUILD_TYPE=Debug ..
make
For testing, have to manually run the binary
../bin/testbamalignment

Automatic testing always crashes:
[100%] Linking CXX executable ../../bin/testbamalignment
CMakeFiles/testbamalignment.dir/testbamalignment.cpp.o: In function `BamAlignmentTest_pathEndSoftBack_Test::TestBody()':
testbamalignment.cpp:(.text+0xa84): undefined reference to `testing::internal::GetBoolAssertionFailureMessage[abi:cxx11](testing::AssertionResult const&, char const*, char const*, char const*)'
testbamalignment.cpp:(.text+0x13a9): undefined reference to `testing::internal::GetBoolAssertionFailureMessage[abi:cxx11](testing::AssertionResult const&, char const*, char const*, char const*)'
CMakeFiles/testbamalignment.dir/testbamalignment.cpp.o: In function `BamAlignmentTest_pathEnd_Test::TestBody()':
testbamalignment.cpp:(.text+0x2efc): undefined reference to `testing::internal::GetBoolAssertionFailureMessage[abi:cxx11](testing::AssertionResult const&, char const*, char const*, char const*)'
testbamalignment.cpp:(.text+0x3720): undefined reference to `testing::internal::GetBoolAssertionFailureMessage[abi:cxx11](testing::AssertionResult const&, char const*, char const*, char const*)'
CMakeFiles/testbamalignment.dir/testbamalignment.cpp.o: In function `BamAlignmentTest_pathEndBack_Test::TestBody()':
testbamalignment.cpp:(.text+0x50be): undefined reference to `testing::internal::GetBoolAssertionFailureMessage[abi:cxx11](testing::AssertionResult const&, char const*, char const*, char const*)'
CMakeFiles/testbamalignment.dir/testbamalignment.cpp.o:testbamalignment.cpp:(.text+0x5921): more undefined references to `testing::internal::GetBoolAssertionFailureMessage[abi:cxx11](testing::AssertionResult const&, char const*, char const*, char const*)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [../bin/testbamalignment] Error 1
make[1]: *** [test/CMakeFiles/testbamalignment.dir/all] Error 2
make: *** [all] Error 2

My solution is to manually edit the configure file: 

enable_testing()
add_subdirectory( src )
add_subdirectory( test )

Comment out: enable_testing(); and add_subdirectory(test)
For production version.

To build documents

cd docs
doxygen 
This will produce html directory for distribution to a web server.

How to make a distribution?
I have added some package functionality

** make package_source **
===================
cd build
rm -rf * # you must remove everything othewise cmake will hung
cmake ..
	1. make package_source
      This is the old way
   2. cpack -G TGZ
   3. cmake --build . --target package_source

=====================
will genrate source distribution in different formats
There is a bug in cmake, you have to clean the build directory 
first before running this command otherwise it will hung 
there forever.

===== to run the test ===

ctest