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= Library Documentation =
= Library Documentation =
Latest Doxygen documentation: <span style="color:#B22222">Coming Soon</span>
Latest Doxygen documentation:
[http://www.sph.umich.edu/csg/mktrost/doxygen/2011_08_23/ 8/23/11 Library Documentation in Doxygen]
Additional documentation: <span style="color:#B22222">Currently outdated, but updates will be coming soon</span>
Additional documentation: <span style="color:#B22222">Currently outdated, but updates will be coming soon</span>
== Using the Library in Your Own Program ==
== Using the Library in Your Own Program ==
=== Using SampleProgram as a starting point ===
=== Starting from a Sample Program ===
[https://github.com/statgen/SampleProgram https://github.com/statgen/SampleProgram] is a simple program demonstrating how to write a tool that uses libStatGen. You can copy SampleProgram and use it as a starting point for your own program.
[https://github.com/statgen/SampleProgram https://github.com/statgen/SampleProgram] is a simple program demonstrating how to write a tool that uses libStatGen and can be used as a starting point for your tool.
SampleProgram has 4 subdirectories:
SampleProgram has 4 subdirectories:
* src - this is where your own program code goes
* src - this is where your own program code goes
* test - this is where your test code goes. Test code can be setup to run with <code>make test</code> to ensure the program works properly.
* test - this is where your test code goes. Test code can be setup to run with <code>make test</code> to ensure the program works properly.
'''Using SampleProgram as a starting point for your tool:'''
# Copy SampleProgram into a directory with your program name (it is the starting point for your own program).
# Update ChangeLog, .gitignore, and README.txt as appropriate.
# Add any necessary copyrights to the copyrights directory.
#* No changes to Makefile should be necessary.
# Update Makefile.inc
## Update the VERSION as necessary.
## Replace all occurrences of <code>SAMPLE_PROGRAM</code> with an all caps name for your program.
##* You can then use the <code>LIB_PATH_<your program name></code> environment variable to specify an alternate path to libStatGen specific for your program. In most cases you will not need to do this.
#* No other updates to Makefile.inc should be necessary.
# Add your program (cpp & h files) to the <code>src</code> directory.
# Update src/Makefile
## Set EXE to your program executable (replacing sampleProgram)
## Set TOOLBASE, SRCONLY, and HDRONLY as appropriate for specifying your program file names.
## Set any of the other optional settings as specified in the sample makefile.
#* No other changes should be necessary to src/Makefile.
# Add your tests to the <code>test</code> directory.
# Update test/Makefile as appropriate for specifying how to compile/run your tests.
=== Working from Scratch ===
=== Working from Scratch ===
When compiling your code, be sure to include the library header files found in libStatgen/include/ and link in the appropriate library (opt, debug, or profile).
When compiling your code, be sure to include the library header files found in libStatgen/include/ and link in the appropriate library (opt, debug, or profile).
