Add links to the documentation in the report. Moved documentation to readthedocs and added extensive module documentation. Change the -deduplication-estimate-bits to a more understandable --duplication-max-stored-fingerprints. Add a small table that lists how many reads are >=Q5, >=Q7 etc. in the per sequence average quality report. The progressbar can track progress through more file formats. The deduplication fingerprint that is used is now configurable from the command line. The deduplication module starts by gathering all sequences rather than half of the sequences. This allows all sequences to be considered using a big enough hash table.