Version 0.84 - June 2013

1. Modified the construction of tool configuration files for tools that are
listed as only outputting to the stream.  If the tool appears as a standalone
task, or at the end of a loop, the tool will write to stdout (and a filename
is defined).

2. The pipeline fastq-bam was added.  This is essentially the same as the
fastq-vcf pipeline, except that the pipeline finishes at the left-aligned
BAM and does not proceed to call variants with FREEBAYES.
Version 0.85 - June 2013

1. Modified some configuration files.
Version 0.85 - June 2013

1. Included bamUtil from the University of Michigan.
Version 0.87 - June 2013

1. Modified build instructions for bamUtil (University of Michigan).
Version 0.88 - June 2013

1. Changed the order of setPaths and checkParameters in gkno.py.  This
ensures that all parameters are checked to see if they are set prior to
attempting to set file paths.
Version 0.89 - June 2013

1. Modified the logic when writing command lines to the makefile.  For tools
that are listed as only outputting to stream, but include instructions for
when not outputting to stream, the logic has changed.  Originally, the output
is a redirection to a file, but for some of the tools, this fails.  The reason
for the failure is under investigation with the tool authors, but as a temporary
fix, the redirection first gets piped through cat, solving the problem.

This should be a temporary fix and removed in future versions.
Merge remote branch 'upstream/master'