Sequali

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+ Fix a small visual bug in the report sidebar.
+ PyGAL report htmls are now fully HTML5 compliant. HTML5 validation has been
made a part of the integration testing.

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+ Image files can now be saved as SVG files.
+ The javascript file for the tooltip highlighting is now embedded in the
html file so no internet access is needed for the functionality.
+ A sidebar with a table of contents is added to the report for easier
navigation.
+ Graph fonts are made a little bigger. Graphs now respond to zooming in and
out on the web page.
+ Enable building on ARM platforms such as M1 macintosh and Aarch64.
+ Speedup the overrepresented sequences module by adding an AVX2 k-mer
construction algorithm.

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+ 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.

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+ Fix a bug in the overrepresented sequence sampling where the fragments from
the back half of the sequence were incorrectly sampled. Leading to the last
fragment being sampled over and over again.

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+ Base the percentage in the overrepresented sequences section on the number
of found fragments divided by the number of sampled sequences. Previously
this was based on the number of sampled fragments, which led to very low
percentages for long read sequences, whilst also being less intuitive to
understand. There were some inconsistencies in the documentation about this
that are now fixed.
+ Add a new `meta` section to the JSON report to allow integration with
`MultiQC <https://github.com/multiqc/MultiQC>`_.
+ Add all nanopore barcode sequences and native adapters to the contaminants.
+ Add native adapters to the adapter search.

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+ Fixed an issue that caused an off by one error if start and end time
of a Nanopore run were at certain intervals.