Cutadapt

-----------------

* :issue:`654`: When determining the error rate for a partial match of an
adapter with ``N`` wildcards, the number of non-N bases was not computed
correctly, which could lead to matches not being found.
* :issue:`546`: Automatically replace ``I`` in adapter sequences with ``N``.
``I`` is used to encode inosine, which matches any base. Contributed by peterjc.
* :issue:`528`: Cutadapt should now no long hang in multicore mode when an error
was raised in a worker process (for example, when an incorrectly formatted
FASTQ file was encountered).

-----------------

* :issue:`624`: You can now combine reading adapter sequences from an external file
with the search parameter notation. For example,
``-a "file:adapters.fasta;min_overlap=5"`` sets the minimum overlap to 5 for all
adapters in ``adapters.fasta``.
* :issue:`361`: When reading 5' adapters from an external file, they can now
all be anchored by using the syntax ``-g ^file:adapters.fasta``
(note the ``^`` before ``file:``).
* :issue:`254`: Finding the *rightmost* 5' adapter occurrence is now supported by using the
``rightmost`` search parameter (the default is to find the leftmost occurrence).
* :issue:`615`: Fix linked adapter statistics for 5' and 3' end not
being reported separated correctly.
* :issue:`616`: Report correct number of quality-trimmed bases when
both ``-q`` and ``--nextseq-trim`` are used.

-----------------

* :issue:`604`, :pr:`608`: The :ref:`alignment algorithm was tweaked <algorithm-indel-scores>`
to penalize indels more and to more accurately pick the leftmost adapter
occurrence if there are multiple. This will normally affect very few
reads, but should generally lead to fewer surprising results in cases
where it matters. Because this changes trimming results, it was appropriate
to bump the major version to 4.
* :issue:`607`: Print an error when an output file was specified
multiple times (for example, for ``--untrimmed-output`` and
``--too-short-output``). Sending output from different filters to
the same file is not supported at the moment.
* :issue:`603`: When ``-e`` was used with an absolute number of errors
and there were ``N`` wildcards in the sequence, the actual number of
allowed errors was too low.
* Speed up quality trimming (both ``-q`` and ``--nextseq-trim``) somewhat.
* Python 3.6 is no longer supported as it is end-of-life.

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* :issue:`600`: Fixed ``{match_sequence}`` placeholder not working when
renaming paired-end reads.

---------------------

* :issue:`437`: Add ``{match_sequence}`` to the placeholders that ``--rename``
accepts. This allows to add the sequence matching an adapter (including
errors) to the read header. An empty string is inserted if there is no match.
* :issue:`589`: Windows wheels are now available on PyPI. That is,
``pip install`` will no longer attempt to compile things, but just install
a pre-compiled binary.
* :issue:`592`: Clarify in documentation and error messages that anchored
adapters need to match in full and that therefore setting an explict
minimum overlap (``min_overlap=``, ``o=``) for them is not possible.

-----------------

* :issue:`555`: Add support for dumping statistics in JSON format using ``--json``.
* :issue:`541`: Add a "Read fate breakdown" section heading to the report, and also
add statistics for reads discarded because of ``--discard-untrimmed`` and
``--discard-trimmed``. With this, the numbers in that section should add up to 100%.
* Add option ``-Q``, which allows to specify a quality-trimming threshold for R2 that is
different from the one for R1.
* :issue:`567`: Add ``noindels`` adapter-trimming parameter. You can now write
``-a "ADAPTER;noindels"`` to disallow indels for a single adapter only.
* :issue:`570`: Fix ``--pair-adapters`` not finding some pairs when reads contain
more than one adapter.
* :issue:`524`: Fix a memory leak when using ``--info-file`` with multiple cores.
* :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.