Changes

From Genome Analysis Wiki
Jump to: navigation, search

C++ Library: libStatGen

324 bytes added, 17:08, 24 March 2011
no edit summary
[[Category:libStatGen]]
== DESCRIPTION ==Open source, freely available (GPL license), easy to use C++ APIs* General Operation Classes including:**File/Stream I/O – uncompressed, BGZF, GZIP, stdin, stdout** String processing** Parameter Parsing* Statistical Genetic Specific Classes including:**Handling Common file formats – SAM/BAM, FASTQ, GLF**Indexed access to BAM files**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
 =Library Documentation == Contents ===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[http://www.sph.umich.edu/csg/mktrost/doxygen/version.0.1.2/ Version 0.1.2 Library Documentation in Doxygen] Possibly out of date documentaitons: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: BAM]] - Classes specific for reading/writing/analyzing SAM/BAM files.
* [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files.
[http://www.sph.umich.edu/csg/mktrost/doxygen/version.0.1.2/ Version 0.1.2 Library Documentation in Doxygen]
= Using the Library =To use the StatGen Library, first download and compile via [[StatGen Download | StatGen Download Instructions]] and [[http://www.sph.umichStatGen Repository#Compile.edu/csg/mktrost/doxygen/march22_2011/ 3/222FBuild | StatGen Compile/11 Library Documentation in DoxygenBuild Instructions]]
== Using the Library ==
To use the StatGenLibrary, first download:
http://genome.sph.umich.edu/wiki/Software#Download
*Build: type make
== Creating programs ==
If you are creating a program, you can start with Makefile.src found at statgen/src/.

Navigation menu