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***Cigar – interpretation and mapping between query and reference
***Cigar – interpretation and mapping between query and reference
***Pileup – structured access to data by individual reference position
***Pileup – structured access to data by individual reference position
Can be used to create your own C++ programs.
Currently the repository is recommended for Unix/Linux users with access to the GNU C++ compiler.
Currently the repository is recommended for Unix/Linux users with access to the GNU C++ compiler.
Here are links to the copyrights for our code and some of the utilities it uses:
Here are links to the copyrights for our code and some of the utilities it uses:
*[https://github.com/statgen/libStatGen/blob/master/general/COPYING Our Copyright GNU GENERAL PUBLIC LICENSE] and [https://github.com/statgen/libStatGen/blob/master/general/LICENSE.txt Our Copyright Note]
*[https://github.com/statgen/libStatGen/blob/master/general/COPYING GNU GENERAL PUBLIC LICENSE] and [https://github.com/statgen/libStatGen/blob/master/general/LICENSE.txt Our Copyright Note]
*[https://github.com/statgen/libStatGen/blob/master/general/LICENSE.twister Copyright for MERSENNE TWISTER (used in Random.cpp)]
*[https://github.com/statgen/libStatGen/blob/master/general/LICENSE.twister Copyright for MERSENNE TWISTER (used in Random.cpp)]
*[https://github.com/statgen/libStatGen/blob/master/samtools/COPYING Samtools Copyright (MIT License)]
*[https://github.com/statgen/libStatGen/blob/master/samtools/COPYING Samtools Copyright (MIT License)]
= Using the Library =
= Using the Library =
== Dependencies ==
* This software requires the following to be installed:
** g++
** development version of zlib (zlib1g-dev on ubuntu)
** openssl and md5 (libssl-dev on ubuntu)
* Compiles on Linux/Unix
== Building the Library ==
== Building the Library ==
</pre>
</pre>
When you just type make, it will by default to make opt.
When you just type make, it will by default to make opt (optimized).
Make all indicates opt, debug, and profile.
Make all indicates opt, debug, and profile.
opt creates libStatGen.a, debug creates libStatGen_debug.a, profile creates libStatGen_profile.a
opt creates <code>libStatGen.a</code>, debug creates <code>libStatGen_debug.a</code>, profile creates <code>libStatGen_profile.a</code>
These libraries are created in the top level libStatGen directory and can then be linked to appropriately for optimized, debugging, or profiling builds.
These libraries are created in the top level libStatGen directory and can then be linked to appropriately for building tools as optimized, debugging, and/or profiling.
== Navigating the Library Subdirectories ==
== Navigating the Library Subdirectories ==
=== 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: libStatGen.a, debug: libStatGen_debug.a, or profile: libStatGen_profile.a).
= Troubleshooting =
If you are having trouble compiling any of the versions, check [[libStatGen Troubleshooting]] for help. If that does not solve your problem, email me for support.
