Version 0.19 - September 2013

1. Further development.  The main update in this commit involves giving all
tools their own configuration file (it was the case that bamtools, for example,
had multiple tools in the same configuration file.  Now bamtools-index etc, have
their own files) and correctly processing them.
Version 0.20 - September 2013

1. Further development.  Merging nodes almost complete.
Version 0.21 - October 2013

1. Completed merging of tool nodes to generate a pipeline.
Version 0.22 - October 2013

1. Dealt with the command line.
Version 0.23 - October 2013

1. Cleaned up unused methods.
Version 0.24 - October 2013

1. Moved some methods from configuration class to nodeMethods. Also fixed
a couple of minor bugs.
Version 0.25 - October 2013

1. Fixed a bug in merging nodes.
Version 0.26 - October 2013

1. Many changes made in moving towards a graph representation.
Version 0.27 - October 2013

1. Modifying the mergeNodes routine to make it cleaner and easier to handle cases
of option nodes associated with filename stubs.  When there are filename stubs, there
can be multiple output files associated with the option node with different names. If
another task uses these files, there has to be a decision about which of the file nodes
are merged and which are left alone.
Version 0.28 - October 2013

1. Completed the merging routine.