C++ Library: libStatGen
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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.
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.