Difference between revisions of "C++ Library: libStatGen"
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Revision as of 16:13, 17 November 2010
DESCRIPTION
Open source, freely available (GPL license), easy to use APIs
- File/Stream I/O – uncompressed, BGZF, GZIP, stdin, stdout
- Common file formats – SAM/BAM, FASTQ, GLF
- Indexed access to BAM files
- Accessors to get/set values
- Utility classes, including:
- Cigar – interpretation and mapping between query and reference
- Pileup – structured access to data by individual reference position
Contents
- 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.
Library Documentation in Doxygen
Download
To use the StatGenLibrary, first download: http://genome.sph.umich.edu/wiki/Software#Download
- Build: type make
- the library is built: statgen/lib/libStatGen.a
- Use Makefile.include to build with the library.
- See examples in statgen/src.
