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.
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
started to add method specific parameters
added ability to use join method specific params
updated the code in ' write_synced_barcodes_fastq' function to better handle cases when we reach the end of the index reads file before the joined paired-ends file. With other minor edits
Resolves issue #1065

Changes the 'simpson_e' calculation to be increase as evenness increases. Reference thread:
https://groups.google.com/forum/#!searchin/qiime-forum/simpsons%2420e/qiime-forum/F7GvTT2Elgw/rU8fnNfLoNMJ
Added another example

Added another test calculation from another ecology lab. Given that the literature definition of this function is unclear, I wanted to have another resource which validates our interpretation.
Change exception formatting and if statements

Formatting the exception messages like this will make the transition to
py3k easier.
started test code for join_paired_ends
cleaning up test code and adding test files