This branch is even with kweitemier:master.
fastq_collapse.py - Discards exact fastq sequence duplicates, preserving the highest average quality score. It also makes a file containing all the duplicated reads. by Kevin Weitemier February 2013 Copyright (c) 2011,2012,2013 Kevin Weitemier. Version 0.03 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. A copy of this license is distributed with the program and available at <http://www.gnu.org/licenses/>. Great effort has been taken to make this software perform its said task, however, this software comes with ABSOLUTELY NO WARRANTY, not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Input - A fastq file where each sequence occupies four (4) lines. Usage: fastq_collapse.py -i INFILE -o OUTFILE [-j JOB_ID]