Branch graph, Version 0.15 - September 2013

1. General development.
Branch graph, Version 0.16 - September 2013

1. Further development to accomodate the merging of nodes in the
configuration class.
Branch graph, Version 0.17 - October 2013

1. Pipeline built by building tools as individual units and then nodes merged
to generate a pipeline.
Branch graph, Version 0.18 - October 2013

1. Complete up to adding command line arguments.
Branch graph, Version 0.19 - October 2013

1. Made sure that values were added to the option nodes for command line arguments set using
the name of a task.  Also ensured that the file nodes values are set to the same values as
the corresponding option node.
Branch graph, Version 0.20 - October 2013

1. Fixed some bugs in adding command line arguments to the nodes.
Branch graph, Version 0.21 - October 2013

1. Fixed some bugs.
Branch graph, Version 0.22 - October 2013

1. More progress towards the graph representation.
Branch graph, Version 0.23 - October 2013

1. Working on modifications to merging the nodes to create the pipeline graph
and the handling of filename stubs.
Branch graph, Version 0.24 - November 2013

1. Added more functionality for handling filename construction and
adding values to nodes.
Branch graph, Version 0.25 - November 2013

1. Fixed a bug when attaching values to nodes.
Branch graph, Version 0.26 - November 2013

1. Finished handling intermediate files.
Branch graph, Version 0.27 - November 2013

1. Dealt with reading in data from multiple runs or internal loops files
    and added the data to the graph nodes.
Branch graph, Version 0.28 - November 2013

1. Ensured that multiple runs/internal loop values were correctly handled in the
case that file stubs are used. For example, if building jump databases with different
values of hash size, there should be as many outputs as there are input hash sizes.
Branch graph, Version 0.29 - November 2013

1. Determined makefile structure and started including routines to write
out data to makefiles. An improvement over the original incarnation of
gkno is that a pipeline can be run in multiple runs mode and gkno will
determine if it needs to be partitioned into phases. For example, phase 1
might consist of building reference files, then phase 2 is multiple
alignment tasks that can be run in parallel. Finally, phase 3 may
collecyt all of the information from phase 2 and perform variant calling
on all of the alignments.
Branch graph, Version 0.29 - November 2013

1. Further development in the makefiles. All commands are written out, omitting
those that shouldn't be (e.g. bamtools-index --out).

2. Progress on running in tool mode.

3. Bug fixes to pipeline usage help.
Branch graph, Version 0.30 - November 2013

1. Updates in support of tool operation.
Branch graph, Version 0.31 - November 2013

1. Handled lists of input files in tool mode.
Branch graph, Version 0.32 - November 2013

1. Minor bug fixes.

2. File paths are attached to files.
Branch graph, Version 0.33 - November 2013

1. Complete rewrite of usage and help information.