v3.5 (2021-09-29)
-----------------
* :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.
v3.4 (2021-03-30)
-----------------
* :issue:`481`: An experimental single-file Windows executable of Cutadapt
is `available for download on the GitHub "releases"
page <https://github.com/marcelm/cutadapt/releases>`_.
* :issue:`517`: Report correct sequence in info file if read was reverse complemented
* :issue:`517`: Added a column to the info file that shows whether the read was
reverse-complemented (if ``--revcomp`` was used)
* :issue:`320`: Fix (again) "Too many open files" when demultiplexing
v3.3:
* :issue:`504`: Fix a crash on Windows.
* :issue:`490`: When ``--rename`` is used with ``--revcomp``, disable adding the
``rc`` suffix to reads that were reverse-complemented.
* Also, there is now a ``{rc}` template variable for the ``--rename`` option, which
is replaced with "rc" if the read was reverse-complemented (and the empty string if not).
* :issue:`512`: Fix issue :issue:`128` once more (the “Reads written” figure in the report
incorrectly included both trimmed and untrimmed reads if ``--untrimmed-output`` was used).
* :issue:`515`: The report is now send to stderr if any output file is
written to stdout
