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[[Category:libStatGen]]
[[Category:libStatGen]]
= DESCRIPTION =
Open source, freely available (GPL license), easy to use APIs
Open source, freely available (GPL license), easy to use C++ APIs
*File/Stream I/O – uncompressed, BGZF, GZIP, stdin, stdout
* General Operation Classes including:
*Common file formats – SAM/BAM, FASTQ, GLF
** File/Stream I/O – uncompressed, BGZF, GZIP, stdin, stdout
**Indexed access to BAM files
** String processing
**Accessors to get/set values
** Parameter Parsing
*Utility classes, including:
* Statistical Genetic Specific Classes including:
**Cigar – interpretation and mapping between query and reference
**Handling Common file formats – SAM/BAM, FASTQ, GLF
**Pileup – structured access to data by individual reference position
***Accessors to get/set values
***Indexed access to BAM files
**Utility classes, including:
***Cigar – interpretation and mapping between query and reference
***Pileup – structured access to data by individual reference position
=== Contents ===
= Library Documentation =
Latest Doxygen documentation:
[http://www.sph.umich.edu/csg/mktrost/doxygen/march22_2011/ 3/22/11 Library Documentation in Doxygen]
[http://www.sph.umich.edu/csg/mktrost/doxygen/version.0.1.2/ Version 0.1.2 Library Documentation in Doxygen]
Possibly out of date documentaitons:
* [[StatGenLibrary: general]] - General classes for file processing and performing common tasks (used by most other libraries).
* [[StatGenLibrary: general]] - General classes for file processing and performing common tasks (used by most other libraries).
* [[StatGenLibrary: BAM]] - Classes specific for reading/writing/analyzing SAM/BAM files.
* [[StatGenLibrary: BAM]] - Classes specific for reading/writing/analyzing SAM/BAM files.
* [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files.
* [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files.
[http://www.sph.umich.edu/csg/mktrost/doxygen/march22_2011/ 3/22/11 Library Documentation in Doxygen]
= Using the Library =
To use the StatGen Library, first download and compile via [[StatGen Download | StatGen Download Instructions]] and [[StatGen Repository#Compile.2FBuild | StatGen Compile/Build Instructions]]
*Build: type make
*Build: type make
= Creating programs =
If you are creating a program, you can start with Makefile.src found at statgen/src/.
If you are creating a program, you can start with Makefile.src found at statgen/src/.
