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
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
code should NOT pass any optional params to the app controller unless user specified, except for '-y'
added more text to parameter help
minor edits to parameter help text