Initial import of source files from previous SVN repository.
Updating git INSTALL instructions, briefly.
Updating installation directions.
Updating installation requirements as well as configuring build system.
Updating copyright information and a brief description of each program.
Updating dutil description and copyright information.
Adding wgsim from samtools and introducing the ability to specify error rates for each color
Updating wgsim for BFAST and BWA/MAQ output.  Since BWA/MAQ specifically
remove the adapter and first color of ABI SOLiD data, this must be
reflected in the simulated reads.
Adding in print usage and different contact details for wgsim
Removing some debugging code from wgsim where the color space was not double encoded.
Moving wgsim to its own folder.
Updating wgsim_eval.pl some more for my own customizations.
Removing obselete option from print usage in wgsim.c
Adding in support for error rates file.
Updating typo in the README file.
Updating wgsim evaluation code to avoid a divide by zero error.
Adding in a pileup evaluator as well as updating some fixes in the wgsim evaluator.
Updating wgsim to support of BFAST and BWA only.
Adding in counter in wgsim
Updating DNAA to be compatible with BFAST 0.6.0.