Add a CITATION file.
Add --quiet option: Do not print a report.
Test --untrimmed-output.
Test on Python 3.4
Refactor paired-end handling a bit.

- Add a PairedSequenceReader class. This is used to iterate
  over paired-end read. It also checks whether reads are
  properly paired.
- Split process_reads() into process_single_reads() and
  process_paired_reads().
- Adjust tests such that identical read names are checked.
reformat help output a bit
Add --untrimmed-paired-output option.

This fixes the use of --untrimmed-output on paired-end reads, which
previously just didn't work because it created unsynchronized paired-end
output files. The options --untrimmed-output and --untrimmed-paired-output
must now either both or not at all be specified when trimming paired-end reads.