Difference between revisions of "C++ Library: libStatGen"
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= Using the Library = | = 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]] | To use the StatGen Library, first download and compile via [[StatGen Download | StatGen Download Instructions]] and [[StatGen Repository#Compile.2FBuild | StatGen Compile/Build Instructions]] | ||
+ | This creates the library: statgen/lib/libStatGen.a | ||
+ | == Creating programs == | ||
+ | After the statgen repository has been created: | ||
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− | + | ''' THIS IS IN THE PROCESS OF BEING UPDATED - CHECK BACK SOON''' | |
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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/. | ||
Revision as of 17:13, 24 March 2011
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
- 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
- Handling Common file formats – SAM/BAM, FASTQ, GLF
Library Documentation
Latest Doxygen documentation: 3/22/11 Library Documentation in Doxygen
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Possibly out of date documentaitons: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: GLF - Classes specific for reading/writing/analyzing GLF files.
- StatGenLibrary: FASTQ - Classes specific for reading/writing/analyzing FastQ files.
Using the Library
To use the StatGen Library, first download and compile via StatGen Download Instructions and StatGen Compile/Build Instructions This creates the library: statgen/lib/libStatGen.a
Creating programs
After the statgen repository has been created:
THIS IS IN THE PROCESS OF BEING UPDATED - CHECK BACK SOON
If you are creating a program, you can start with Makefile.src found at statgen/src/.
(If you are creating a program in a directory outside of statgen/src, you may need additional modifications.)
Example: creating statgen/src/myprog/
- cd statgen/src/myprog
- ln -s ../Makefile.src Makefile
- cp ../bam/Makefile.tool .
- Update Makefile.tool for your specific program.
- You may need settings beyond were set in statgen/src/bam/Makefile.tool. See Makefile.src for what settings you can use.