Cutadapt

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

* :issue:`441`: Add a ``--max-ee`` (or ``--max-expected-errors``) option
for filtering reads whose number of expected errors exceeds the given
threshold. The idea comes from
`Edgar et al. (2015) <https://academic.oup.com/bioinformatics/article/31/21/3476/194979>`_.
* :issue:`438`: The info file now contains the ``rc`` suffix that is added to
the names of reverse-complemented reads (with ``--revcomp``).
* :issue:`448`: ``.bz2`` and ``.xz`` output wasn’t possible in multi-core mode.

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

* :issue:`220`: With option ``--revcomp``, Cutadapt now searches both the read
and its reverse complement for adapters. The version that matches best is
kept. This can be used to “normalize” strandedness.
* :issue:`430`: ``--action=lowercase`` now works with linked adapters
* :issue:`431`: Info files can now be written even for linked adapters.

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

* :issue:`427`: Multicore is now supported even when using ``--info-file``,
``--rest-file`` or ``--wildcard-file``. The only remaining feature that
still does not work with multicore is now demultiplexing.
* :issue:`290`: When running on a single core, Cutadapt no longer spawns
external ``pigz`` processes for writing gzip-compressed files. This is a first
step towards ensuring that using ``--cores=n`` uses only at most *n* CPU
cores.
* This release adds support for Python 3.8.

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

* :issue:`395`: Do not show animated progress when ``--quiet`` is used.
* :issue:`399`: When two adapters align to a read equally well (in terms
of the number of matches), prefer the alignment that has fewer errors.
* :issue:`401` Give priority to adapters given earlier on the command
line. Previously, the priority was: All 3' adapters, all 5' adapters,
all anywhere adapters. In rare cases this could lead to different results.
* :issue:`404`: Fix an issue preventing Cutadapt from being used on Windows.
* This release no longer supports Python 3.4 (which has reached end of life).

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

* :issue:`391`: Multicore is now supported even when using
``--untrimmed-output``, ``--too-short-output``, ``--too-long-output``
or the corresponding ``...-paired-output`` options.
* :issue:`393`: Using ``--info-file`` no longer crashes when processing
paired-end data. However, the info file itself will only contain results
for R1.
* :issue:`394`: Options ``-e``/``--no-indels``/``-O`` were ignored for
linked adapters
* :issue:`320`: When a “Too many open files” error occurs during
demultiplexing, Cutadapt can now automatically raise the limit and
re-try if the limit is a “soft” limit.

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

* :issue:`292`: Implement support for demultiplexing paired-end reads that use
:ref:`combinatorial indexing (“combinatorial demultiplexing”)
<combinatorial-demultiplexing>`.
* :pr:`384`: Speed up reading compressed files by requiring an xopen version
that uses an external pigz process even for *reading* compressed input files
(not only for writing).
* :issue:`381`: Fix ``--report=minimal`` not working.
* :issue:`380`: Add a ``--fasta`` option for forcing that FASTA is written
to standard output even when input is FASTQ. Previously, forcing
FASTA was only possible by providing an output file name.