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
updated to make uclust the default taxonomy assigner. also updated ancient documentation
updated to make uclust the default taxonomy assigner
updated to make uclust the default taxonomy assigner
updated changelog
updated unit tests to reflect uclust as the default tax assigner
updated unit tests to reflect uclust as the default tax assigner
preparing for updated output files
updated test output files
preparing for updated output files