Version 0.73 - May 2013

1. Allowed the 'additional files' section of the tool configuration files to
include a list of files that are outputted by the tool.

2. Handled PHONY outputs.

3. Added a script to parse 1000 Genomes sequence index files and generate
input files for the align-pe pipeline.
Version 0.74 - May 2013

1. Modified the multiple runs such that the format of the input file is
identical to that for the internal runs.
Version 0.75 - May 2013

1. When writing arguments to the command lines in the makefiles, strings
are now checked to see if they contain spaces.  If so, the argument is
written in quotation marks.  This is a result of the 1000G sequence index
parsing as some of the fields (e.g. the sequencing platform) are often
listed including spaces.
Version 0.76 - May 2013

1. Included a check to see if the --internal-loop argument is set for pipelines
where no internal loop information is provided in the configuration file.
Merge remote-tracking branch 'origin/master'