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
Adding more information to open reference log
Add sanity checks to parse_coords ( fixes #982 )

Add a couple checks to the coordinates parser, doing this prevents the
parser to load distance matrices seamlessly. Specifically the function
will now check for:
    - First line being the number of vectors.
    - Second to last line being eigenvalues.
    - Last line being the percentage of variation explained.

When these conditions are not mete a `QiimeParseError` exception is
raised; the test suite was extended to check it raises these errors on
different cases.
Remove extra percent sign in coordinates string

This percent sign would have only be needed if the string was being
formatted.
Fix #1092 and Fix #979
Added 2 histogram formatting code to qiime/format.py and unit test, in preparation for use with new quality_filter_fasta.py code
started implementing code for joining paired ends
fixed typo in scripts/join_paired_ends.py
cleaned up 'join_paired_ends.py' started code for index reads file handling
added prototype code to remove unused barcodes
minor edits
Addressing Greg's comments
Merge branch 'master' of git://github.com/qiime/qiime into upstream_log
rewrote code that writes new index file