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
Move conversion code to stand-alone lib
Fix import statement
Fix code guidelines
Correct Sample ids to be MIENS compliant
Fix #1092 and Fix #979
Merge branch 'master' of https://github.com/qiime/qiime into issue-1092
Removing Unifrac file conversion code as it has been ported to the FastUnfrac repo
Merge branch 'master' of git://github.com/qiime/qiime into MIENS
Ooops, forgot to delete the qiime_test_data folder for the convert_unifrac_sample_mapping_to_otu_table script
simplified ul_confidence_bounds

* precomputed values are now a table instead of elifs
* two possible returns
* cyclomatic complexity down from a score of 60 to 8
added credit
simplified entropy check
rework of filter_alignment.apply_lane_mask_and_gap_filter

* no more temporary files
* cyclomatic complexity down from 34 to 9
* much smaller method
Rename script interface arguments

The naming is more standard now
Fix different aspects of the documentation

Mainly:
    - Made all lines fewer than 80 columns.
    - Change strings in the documentation to reflect the actual
      filenames that these are processing (it seems that it was still
      pointing to .txt contingency tables)

Fixes #304
Add note about the interface change.
Fixes issue with emtpy tables if data points are missing. Fixes #1197