Difference between revisions of "C++ Library: libStatGen"
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Jump to navigationJump to search| Line 3: | Line 3: | ||
[[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 |
| − | * | + | ** 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 | ||
| − | == | + | |
| + | = 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| + | Possibly out of date documentaitons: | ||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. | ||
| Line 19: | Line 30: | ||
* [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ 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 | StatGen Download Instructions]] and [[StatGen Repository#Compile.2FBuild | StatGen Compile/Build Instructions]] | ||
| − | |||
| − | |||
| − | |||
*Build: type make | *Build: type make | ||
| Line 33: | Line 41: | ||
| − | + | = 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/. | ||
Revision as of 17:08, 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
- Build: type make
- the library is built: statgen/lib/libStatGen.a
- Use Makefile.include to build with the library.
- See examples in statgen/src.
Creating programs
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.
