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.
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
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
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
added minor test case for set_min_overlap
addressed most code review comments
updated example files to fis fastq-join output issue
adding more files to fix fastq-join output issue
copied files to pycogent_backports, fixed import statements
added seqprep test files