Add a --version option to create_snp_matrix.  Improve version logging in scripts.
HPC performance improvements. Create symlinks to files in the work dir, rather than copying large seq files.  Sort sample directories by size and process the largest first to diminish the adverse affects of large stragglers on the HPC cluster.
Add the referenceSNP.fasta file to the supplied lambda virus expected results data set.
Add timestamps for each step in the pipeline.
Use scratch storage because isilob does not support symlinks.
Fix log messages.
Add reproducible results page to the documentation.
Rearchitect pipeline removing the python multiprocessing and running the snp pileup with python code instead of SAMtools.  Split the python create_snp_matrix.py into 4 smaller and simpler scripts.
Merge branch 'nopileup'
Added hashes for agona data. Need review for correctness.
Updated usage to include more info on doing Agona test case.
Updated documentation in reproducible.rst.
More work on reproducible.rst.
copy_snppipeline_data.py script handles existing destination directories more
sensibly now.
Fix diagnostic logging message.
Merge branch 'AddDocumentation'
Merge branch 'master' of /home/hugh.rand/mnt/biob/svn/Biostats/rand/repo/snppipeline
Commit doc changes to master branch.
Updated Agona data set expected results.
* Changed shell scripts to parse command line arguments with getopts.
* Changed the alignSampleToReference.sh script to specify the number of CPU cores with
  the -p flag, rather than a positional argument.  By default, all CPU cores are
  utilized during the alignment.
* Changed the alignSampleToReference.sh script to expect the full file name of the reference
  including the fasta extension, if any.
* Changed the prepReference.sh script to expect the full file name of the reference
  including the fasta extension, if any.
* Changed the prepSamples.sh script to expect the full file name of the reference
  including the fasta extension, if any.
* Changed test_from_scratch.sh to handle fastq, fq, or compressed gz files.