hpg-libs

C libraries for the High Performance Genomics (HPG) project:

• aligners: HPC implementation of two widely used sequence aligners: Burrows-Whheler Transform (BWT) and Smith-Waterman (SW)
• bioinfo-libs: several data format parsers: gff, bam, vcf, bed, ...
• common-libs: several common utilities for logs, string manipulation, workflows execution, ...
• containers: several data structures : array_list, linked_list, ... other have been collected from different sources such as cprops or khash.
• math: Statistics and algebra functions

Each library must be compiled independently using SCons. A static library file (.a) will be generated as a result in c/build/ folder.

BUILDING Scons is used as building system, to build the library download 'next' branch (for the most recent library), and execute:

$ scons

GCC4.4+ is the only requirement.

DOCUMENTATION You can find more info about HPG project and bioinfo-libs at:

http://wiki.opencb.org/projects/hpg/doku.php

CONTACT You can contact any of the following developers:

• Joaquin Tarraga ([email protected])
• Cristina Y. Gonzalez ([email protected])
• Ignacio Medina ([email protected])
• Hector Martinez ([email protected])