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

Library Documentation

Possibly out of date documentaitons: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.

To use the StatGen Library, first download and compile via StatGen Download Instructions and StatGen Compile/Build Instructions

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.