MODIFIED, map_reads_to_reference supports choice of genetic_code

Modified the script with a --genetic_code option and modified the library
code to be aware of the option. Also changed the test code to include
the new option.
Merge branch 'map_reads_to_reference' of github.com:adamrp/qiime into map_reads_to_reference
modified NCBI web reference

URL is now more descriptive
Make denoise_wrapper work again after using the fancy existing_filepaths option parser, which broke the code.
Use 'existing_filepaths' option in denoiser.py
Added parameters for max walltime, cpus, and nodes
Corrected type of "-w" and fixed the concat of walltime in make_jobs
removed extraneous arguments from qcli calls and cast opts.max_walltime to string
Corrected default type of -w
Corrected version and status
Merge pull request #1050 from ebolyen/issue_1048

Issue 1048
added code and test to extract sample ids associated with state changes in an individual

to support pre/post (or paired difference) tests
updated test function name
updated to filter out individuals that don't have data at all states
added function to extract mapping file metadata category associated with different states
added test cases
more extensive tests and a bug fix
more extensive tests
ugly, but first working version of the script
cleaned up output plots