C++ Library: libStatGen

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/

1. cd statgen/src/myprog
2. ln -s ../Makefile.src Makefile
3. cp ../bam/Makefile.tool .
4. 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.

Upcoming Capabilities

• SAM/BAM support conversion between '=' and the base in a sequence
• BAM to FASTQ