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[[Category:libStatGen]]
[[Category:libStatGen]]
= DESCRIPTION =
= Description =
Open source, freely available (GPL license), easy to use C++ APIs
Open source, freely available (GPL license), easy to use C++ APIs
* General Operation Classes including:
* General Operation Classes including:
** String processing
** String processing
** Parameter Parsing
** Parameter Parsing
* Statistical Genetic Specific Classes including:
* '''Statistical Genetic Specific Classes''' including:
**Handling Common file formats – SAM/BAM, FASTQ, GLF
**Handling Common file formats – SAM/BAM, FASTQ, GLF, VCF (coming soon)
***Accessors to get/set values
***Accessors to get/set values
***Indexed access to BAM files
***Indexed access to BAM files
***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
= Where to Find It =
libStatGen can be found at: [https://github.com/statgen/libStatGen https://github.com/statgen/libStatGen]
You can both browse and download the library at that address.
This is also a git repository. You can create your own git clone from this location:
git clone https://github.com/statgen/libStatGen.git
or
git clone git://github.com/statgen/libStatGen.git
Either of these commands create a directory called <code>libStatGen</code> in the current directory.
If you decide to use git, but need a refresher, see [[How To Use Git]] or [https://statgen.sph.umich.edu/wiki/How_To_Use_Git Notes on how to use git] (if you have access)
= What has changed =
The <code>pipeline</code> and <code>statgen</code> repositories have been deprecated, so please update to our new framework.
libStatGen is the new git repository for our library code.
There are now separate repositories for specific tools/groups of tools, allowing us to track everything separately so it is easier to follow changes that impact a specific tool or the library in general.
= Library Documentation =
= Library Documentation =
Latest Doxygen documentation:
Latest Doxygen documentation: <span style="color:#B22222">Coming Soon</span>
[http://www.sph.umich.edu/csg/mktrost/doxygen/march22_2011/ 3/22/11 Library Documentation in Doxygen]
Additional documentation: <span style="color:#B22222">Currently outdated, but updates will be coming soon</span>
* [[libStatGen: general]] - General classes for file processing and performing common tasks (used by most other libraries).
* [[libStatGen: BAM]] - Classes specific for reading/writing/analyzing SAM/BAM files.
* [[libStatGen: GLF]] - Classes specific for reading/writing/analyzing GLF files.
* [[libStatGen: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files.
= Using the Library =
== Building the Library ==
If you type make help, you get the build options.
<pre>
Makefile help
-------------
Type... To...
make Compile opt
make help Display this help screen
make all Compile everything (opt, debug, & profile)
make opt Compile optimized
make debug Compile for debug
make profile Compile for profile
make clean Delete temporary files
make test Execute tests (if there are any)
</pre>
When you just type make, it will by default to make opt.
Make all indicates opt, debug, and profile.
opt creates libStatGen.a, debug creates libStatGen_debug.a, profile creates libStatGen_profile.a
These libraries are created in the top level libStatGen directory and can then be linked to appropriately for optimized, debugging, or profiling builds.
== Navigating the Library Subdirectories ==
* [[StatGenLibrary: general]] - General classes for file processing and performing common tasks (used by most other libraries).
Under the main libStatGen repository, there are:
* [[StatGenLibrary: BAM]] - Classes specific for reading/writing/analyzing SAM/BAM files.
*bam - library code for operating on bam files.
* [[StatGenLibrary: GLF]] - Classes specific for reading/writing/analyzing GLF files.
*copyrights - copyrights for the library and any code included with it.
* [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files.
*fastq - library code for operating on fastq files.
*general - library code for general operations
*glf - library code for operating on glf files.
*include - after compiling, the library headers are linked here
*Makefiles - directory containing Makefiles that are used in the library and can be used for developing programs using the library
*samtools - library code used from samtools
After Compiling: libStatGen.a, libStatGen_debug.a, libStatGen_profile.a are created at the top level.
=== bam, fastq, general, glf, samtools ===
Object files are placed in an obj directory under each subdirectory with debug & profile objects in obj/debug and obj/profile.
Most also have a test directory. Tests are executed by running <code>make test</code>
=== Makefiles ===
This directory contains base makefiles and makefile settings that are used by the library and by programs being written to use the library.
== Using the Library in Your Own Program ==
<span style="color:#B22222">Coming Soon</span>
''' Below are the outdated instructions for <code>statgen</code>
In the following instructions/comments:
In the following instructions/comments:
* replace STATGEN_DIR with the path to where the statgen directory is located (does not include statgen/).
* replace STATGEN_DIR with the path to where the statgen directory is located (does not include statgen/).
