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| [[Category:libStatGen]] | | [[Category:libStatGen]] |
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− | == DESCRIPTION ==
| + | = 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 |
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− | === 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| + | Possibly out of date documentaitons: |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. |
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| * [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files. | | * [[StatGenLibrary: FASTQ]] - Classes specific for reading/writing/analyzing FastQ files. |
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− | [http://www.sph.umich.edu/csg/mktrost/doxygen/version.0.1.2/ Version 0.1.2 Library Documentation in Doxygen]
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− | [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]] |
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− | == Using the Library ==
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− | To use the StatGenLibrary, first download:
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− | http://genome.sph.umich.edu/wiki/Software#Download
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| *Build: type make | | *Build: type make |
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− | == Creating programs ==
| + | = 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/. |
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