Cutadapt

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* Add read modification option ``--length`` (short: ``--l``), which will
shorten each read to the given length.
* Cutadapt will no longer complain that it has nothing to do when you do not
give it any adapters. For example, you can use this to convert file formats:
``cutadapt -o output.fasta input.fastq.gz`` converts FASTQ to FASTA.
* The ``xopen`` module for opening compressed files was moved to a `separate
package on PyPI <https://pypi.python.org/pypi/xopen>`_.

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

* The ``--interleaved`` option no longer requires that both input and output
is interleaved. It is now possible to have two-file input and interleaved
output, and to have interleaved input and two-file output.
* Fix issue 202: First and second FASTQ header could get out of sync when
options modifying the read name were used.

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

* Added a new “linked adapter” type, which can be used to search for a 5' and a
3' adapter at the same time. Use ``-a ADAPTER1...ADAPTER2`` to search
for a linked adapter. ADAPTER1 is interpreted as an anchored 5' adapter, which
is searched for first. Only if ADAPTER1 is found will ADAPTER2 be searched
for, which is a regular 3' adapter.
* Added experimental ``--nextseq-trim`` option for quality trimming of NextSeq
data. This is necessary because that machine cannot distinguish between G and
reaching the end of the fragment (it encodes G as 'black').
* Even when trimming FASTQ files, output can now be FASTA (quality values are
simply dropped). Use the ``-o``/``-p`` options with a file name that ends in
``.fasta`` or ``.fa`` to enable this.
* Cutadapt does not bundle pre-compiled C extension modules (``.so`` files)
anymore. This affects only users that run cutadapt directly from an unpacked
tarball. Install through ``pip`` or ``conda`` instead.
* Fix issue 167: Option ``--quiet`` was not entirely quiet.
* Fix issue 199: Be less strict when checking for properly-paired reads.
* This is the last version of cutadapt to support Python 2.6. Future versions
will require at least Python 2.7.

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

* Added ``--pair-filter`` option, which :ref:`modifies how filtering criteria
apply to paired-end reads <filtering-paired>`
* Add ``--too-short-paired-output`` and ``--too-long-paired-output`` options.
* Fix incorrect number of trimmed bases reported if ``--times`` option was used.

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

* Indels in the alignment can now be disabled for all adapter types (use
``--no-indels``).
* Quality values are now printed in the info file (``--info-file``)
when trimming FASTQ files. Fixes issue 144.
* Options ``--prefix`` and ``--suffix``, which modify read names, now accept the
placeholder ``{name}`` and will replace it with the name of the found adapter.
Fixes issue 104.
* Interleaved FASTQ files: With the ``--interleaved`` switch, paired-end reads
will be read from and written to interleaved FASTQ files. Fixes issue 113.
* Anchored 5' adapters can now be specified by writing ``-a SEQUENCE...`` (note
the three dots).
* Fix ``--discard-untrimmed`` and ``--discard-trimmed`` not working as expected
in paired-end mode (issue 146).
* The minimum overlap is now automatically reduced to the adapter length if it
is too large. Fixes part of issue 153.
* Thanks to Wolfgang Gerlach, there is now a Dockerfile.
* The new ``--debug`` switch makes cutadapt print out the alignment matrix.

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

* Fix issue 95: Untrimmed reads were not listed in the info file.
* Fix issue 138: pip install cutadapt did not work with new setuptools versions.
* Fix issue 137: Avoid a hang when writing to two or more gzip-compressed
output files in Python 2.6.