CHANGES.rst

@@ -2,6 +2,106 @@
 Changes
 =======
 
+v2.3 (2019-04-25)
+-----------------
+
+* :issue:`378`: The ``--pair-adapters`` option, added in version 2.1, was
+  not actually usable for demultiplexing.
+
+
+v2.2 (2019-04-20)
+---------------------
+
+* :issue:`376`: Fix a crash when using anchored 5' adapters together with
+  ``--no-indels`` and trying to trim an empty read.
+* :issue:`369`: Fix a crash when attempting to trim an empty read using a ``-g``
+  adapter with wildcards.
+
+v2.1 (2019-03-15)
+-----------------
+
+* :issue:`366`: Fix problems when combining ``--cores`` with
+  reading from standard input or writing to standard output.
+* :issue:`347`: Support :ref:`“paired adapters” <paired-adapters>`. One use case is
+  demultiplexing Illumina *Unique Dual Indices* (UDI).
+
+v2.0 (2019-03-06)
+-----------------
+
+This is a major new release with lots of bug fixes and new features, but
+also some backwards-incompatible changes. These should hopefully
+not affect too many users, but please make sure to review them and
+possibly update your scripts!
+
+Backwards-incompatible changes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* :issue:`329`: Linked adapters specified with ``-a ADAPTER1...ADAPTER2``
+  are no longer anchored by default. To get results consist with the old
+  behavior, use ``-a ^ADAPTER1...ADAPTER2`` instead.
+* Support for colorspace data was removed. Thus, the following command-line
+  options can no longer be used: ``-c``, ``-d``, ``-t``, ``--strip-f3``,
+  ``--maq``, ``--bwa``, ``--no-zero-cap``.
+* “Legacy mode” has been removed. This mode was enabled under certain
+  conditions and would change the behavior such that the read-modifying options
+  such as ``-q`` would only apply to the forward/R1 reads. This was necessary
+  for compatibility with old Cutadapt versions, but became increasingly
+  confusing.
+* :issue:`360`: Computation of the error rate of an adapter match no longer
+  counts the ``N`` wildcard bases. Previously, an adapter like ``N{18}CC``
+  (18 ``N`` wildcards followed by ``CC``) would effectively match
+  anywhere because the default error rate of 0.1 (10%) would allow for
+  two errors. The error rate of a match is now computed as
+  the number of non-``N`` bases in the matching part of the adapter
+  divided by the number of errors.
+* This release of Cutadapt requires at least Python 3.4 to run. Python 2.7
+  is no longer supported.
+
+Features
+~~~~~~~~
+
+* A progress indicator is printed while Cutadapt is working. If you redirect
+  standard error to a file, the indicator is disabled.
+* Reading of FASTQ files has gotten faster due to a new parser. The FASTA
+  and FASTQ reading/writing functions are now available as part of the
+  `dnaio library <https://github.com/marcelm/dnaio/>`_. This is a separate
+  Python package that can be installed independently from Cutadapt.
+  There is one regression at the moment: FASTQ files that use a second
+  header (after the "+") will have that header removed in the output.
+* Some other performance optimizations were made. Speedups of up to 15%
+  are possible.
+* Demultiplexing has become a lot faster :ref:`under certain conditions <speed-up-demultiplexing>`.
+* :issue:`335`: For linked adapters, it is now possible to
+  :ref:`specify which of the two adapters should be required <linked-override>`,
+  overriding the default.
+* :issue:`166`: By specifying ``--action=lowercase``, it is now possible
+  to not trim adapters, but to instead convert the section of the read
+  that would have been trimmed to lowercase.
+
+Bug fixes
+~~~~~~~~~
+
+* Removal of legacy mode fixes also :issue:`345`: ``--length`` would not enable
+  legacy mode.
+* The switch to ``dnaio`` also fixed :issue:`275`: Input files with
+  non-standard names now no longer lead to a crash. Instead the format
+  is now recognized from the file content.
+* Fix :issue:`354`: Sequences given using ``file:`` can now be unnamed.
+* Fix :issue:`257` and :issue:`242`: When only R1 or only R2 adapters are given, the
+  ``--pair-filter`` setting is now forced to ``both`` for the
+  ``--discard-untrimmed`` (and ``--untrimmed-(paired-)output``) filters.
+  Otherwise, with the default ``--pair-filter=any``, all pairs would be
+  considered untrimmed because one of the reads in the pair is always
+  untrimmed.
+
+Other
+~~~~~
+
+* :issue:`359`: The ``-f``/``--format`` option is now ignored and a warning
+  will be printed if it is used. The input file format is always
+  auto-detected.
+
+
 v1.18 (2018-09-07)
 ------------------
 

LICENSE

-Copyright (c) 2010-2018 Marcel Martin <marcel.martin@scilifelab.se>
+Copyright (c) 2010-2019 Marcel Martin <marcel.martin@scilifelab.se>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

-include CHANGES.rst
-include CITATION
-include LICENSE
-include doc/*.rst
-include doc/conf.py
-include doc/Makefile
-include versioneer.py
-include src/cutadapt/*.c
-include src/cutadapt/*.pyx
-include tests/utils.py
-include tests/test_*.py
-graft tests/data
-graft tests/cut

PKG-INFO

-Metadata-Version: 1.1
+Metadata-Version: 2.1
 Name: cutadapt
-Version: 1.18
+Version: 2.3
 Summary: trim adapters from high-throughput sequencing reads
 Home-page: https://cutadapt.readthedocs.io/
 Author: Marcel Martin
 Author-email: marcel.martin@scilifelab.se
 License: MIT
-Description-Content-Type: UNKNOWN
 Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master
             :target: https://travis-ci.org/marcelm/cutadapt
         
@@ -14,7 +13,7 @@ Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master
             :target: https://pypi.python.org/pypi/cutadapt
         
         ========
-        cutadapt
+        Cutadapt
         ========
         
         Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
@@ -35,7 +34,7 @@ Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master
         Cutadapt comes with an extensive suite of automated tests and is available under
         the terms of the MIT license.
         
-        If you use cutadapt, please cite
+        If you use Cutadapt, please cite
         `DOI:10.14806/ej.17.1.200 <http://dx.doi.org/10.14806/ej.17.1.200>`_ .
         
         
@@ -56,6 +55,7 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python :: 2.7
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.4
+Provides-Extra: dev

README.rst

@@ -5,7 +5,7 @@
     :target: https://pypi.python.org/pypi/cutadapt
 
 ========
-cutadapt
+Cutadapt
 ========
 
 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
@@ -26,7 +26,7 @@ also just demultiplex your input data, without removing adapter sequences at all
 Cutadapt comes with an extensive suite of automated tests and is available under
 the terms of the MIT license.
 
-If you use cutadapt, please cite
+If you use Cutadapt, please cite
 `DOI:10.14806/ej.17.1.200 <http://dx.doi.org/10.14806/ej.17.1.200>`_ .
 
 

debian/changelog

+python-cutadapt (2.3-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Liubov Chuprikova <chuprikovalv@gmail.com>  Fri, 28 Jun 2019 19:07:03 +0200
+
 python-cutadapt (1.18-1) unstable; urgency=medium
 
   * New upstream version

doc/algorithms.rst

@@ -9,7 +9,7 @@ Adapter alignment algorithm
 ===========================
 
 Since the publication of the `EMBnet journal application note about
-cutadapt <http://dx.doi.org/10.14806/ej.17.1.200>`_, the alignment algorithm
+Cutadapt <http://dx.doi.org/10.14806/ej.17.1.200>`_, the alignment algorithm
 used for finding adapters has changed significantly. An overview of this new
 algorithm is given in this section. An even more detailed description is
 available in Chapter 2 of my PhD thesis `Algorithms and tools for the analysis
@@ -37,7 +37,7 @@ has the disadvantage that they are not at all intuitive: What does a total score
 of *x* mean? Is that good or bad? How should a threshold be chosen in order to
 avoid finding alignments with too many errors?
 
-For cutadapt, the adapter alignment algorithm uses *unit costs* instead.
+For Cutadapt, the adapter alignment algorithm uses *unit costs* instead.
 This means that mismatches, insertions and deletions are counted as one error, which
 is easier to understand and allows to specify a single parameter for the
 algorithm (the maximum error rate) in order to describe how many errors are
@@ -75,7 +75,7 @@ overlaps that are actually allowed by the adapter type are actually considered.
 Quality trimming algorithm
 --------------------------
 
-The trimming algorithm implemented in cutadapt is the same as the one used by
+The trimming algorithm implemented in Cutadapt is the same as the one used by
 BWA, but applied to both
 ends of the read in turn (if requested). That is: Subtract the given cutoff
 from all qualities; compute partial sums from all indices to the end of the

doc/colorspace.rst

-.. _colorspace:
-
-Colorspace reads
-================
-
-Cutadapt was designed to work with colorspace reads from the ABi SOLiD
-sequencer. Colorspace trimming is activated by the ``--colorspace``
-option (or use ``-c`` for short). The input reads can be given either:
-
--  in a FASTA file (typically extensions ``.csfasta`` or ``.csfa``)
--  in a FASTQ file
--  in a ``.csfasta`` and a ``.qual`` file (this is the native SOLiD
-   format). That is, cutadapt expects *two* file names in this case.
-
-In all cases, the colors must be represented by the characters 0, 1, 2,
-3. Here is an example input file in ``.fastq`` format that is accepted::
-
-    @1_13_85_F3
-    T110020300.0113010210002110102330021
-    +
-    7&9<&77)& <7))%4'657-1+9;9,.<8);.;8
-    @1_13_573_F3
-    T312311200.3021301101113203302010003
-    +
-    6)3%)&&&& .1&(6:<'67..*,:75)'77&&&5
-
-Further example input files can be found in the cutadapt distribution at
-``tests/data/solid.*``. The ``.csfasta``/``.qual`` file format is
-automatically assumed if two input files are given to cutadapt, and when no
-paired-end trimming options are used.
-
-Cutadapt always converts input data given as a pair of FASTA/QUAL files to FASTQ.
-
-In colorspace mode, the adapter sequences given to the ``-a``, ``-b``
-and ``-g`` options can be given both as colors or as nucleotides. If
-given as nucleotides, they will automatically be converted to
-colorspace. For example, to trim an adapter from ``solid.csfasta`` and
-``solid.qual``, use this command-line::
-
-    cutadapt -c -a CGCCTTGGCCGTACAGCAG solid.csfasta solid.qual > output.fastq
-
-In case you know the colorspace adapter sequence, you can also write
-``330201030313112312`` instead of ``CGCCTTGGCCGTACAGCAG``, and the result
-is the same.
-
-Ambiguity in colorspace
------------------------
-
-The ambiguity of colorspace encoding leads to some effects to be aware
-of when trimming 3' adapters from colorspace reads. For example, when
-trimming the adapter ``AACTC``, cutadapt searches for its
-colorspace-encoded version ``0122``. But also ``TTGAG``, ``CCAGA`` and
-``GGTCT`` have an encoding of ``0122``. This means that effectively four
-different adapter sequences are searched and trimmed at the same time.
-There is no way around this, unless the decoded sequence were available,
-but that is usually only the case after read mapping.
-
-The effect should usually be quite small. The number of false positives
-is multiplied by four, but with a sufficiently large overlap (3 or 4 is
-already enough), this is still only around 0.2 bases lost per read on
-average. If inspecting k-mer frequencies or using small overlaps, you
-need to be aware of the effect, however.
-
-
-Double-encoding, BWA and MAQ
-----------------------------
-
-The read mappers MAQ and BWA (and possibly others) need their colorspace
-input reads to be in a so-called "double encoding". This simply means
-that they cannot deal with the characters 0, 1, 2, 3 in the reads, but
-require that the letters A, C, G, T be used for colors. For example, the
-colorspace sequence ``0011321`` would be ``AACCTGC`` in double-encoded
-form. This is not the same as conversion to basespace! The read is still
-in colorspace, only letters are used instead of digits. If that sounds
-confusing, that is because it is.
-
-Note that MAQ is unmaintained and should not be used in new projects.
-
-BWA’s colorspace support was dropped in versions more recent than 0.5.9,
-but that version works well.
-
-When you want to trim reads that will be mapped with BWA or MAQ, you can
-use the ``--bwa`` option, which enables colorspace mode (``-c``),
-double-encoding (``-d``), primer trimming (``-t``), all of which are
-required for BWA, in addition to some other useful options.
-
-The ``--maq`` option is an alias for ``--bwa``.
-
-
-Colorspace examples
--------------------
-
-To cut an adapter from SOLiD data given in ``solid.csfasta`` and
-``solid.qual``, to produce MAQ- and BWA-compatible output, allow the
-default of 10% errors and write the resulting FASTQ file to
-output.fastq::
-
-    cutadapt --bwa -a CGCCTTGGCCGTACAGCAG solid.csfasta solid.qual > output.fastq
-
-Instead of redirecting standard output with ``>``, the ``-o`` option can
-be used. This also shows that you can give the adapter in colorspace and
-how to use a different error rate::
-
-    cutadapt --bwa -e 0.15 -a 330201030313112312 -o output.fastq solid.csfasta solid.qual
-
-This does the same as above, but produces BFAST-compatible output,
-strips the \_F3 suffix from read names and adds the prefix "abc:" to
-them::
-
-    cutadapt -c -e 0.15 -a 330201030313112312 -x abc: --strip-f3 solid.csfasta solid.qual > output.fastq
-
-
-Bowtie
-------
-
-Quality values of colorspace reads are sometimes negative. Bowtie gets
-confused and prints this message::
-
-    Encountered a space parsing the quality string for read xyz
-
-BWA also has a problem with such data. Cutadapt therefore converts
-negative quality values to zero in colorspace data. Use the option
-``--no-zero-cap`` to turn this off.
-
 .. _sra-fastq:
+.. _colorspace:
 
-Sequence Read Archive
----------------------
-
-The Sequence Read Archive provides files in a special "SRA" file format. When
-the ``fastq-dump`` program from the sra-toolkit package is used to convert
-these ``.sra`` files to FASTQ format, colorspace reads will get an extra
-quality value in the beginning of each read. You may get an error like this::
-
-    cutadapt: error: In read named 'xyz': length of colorspace quality
-    sequence (36) and length of read (35) do not match (primer is: 'T')
+Colorspace
+==========
 
-To make cutadapt ignore the extra quality base, add ``--format=sra-fastq`` to
-your command-line, as in this example::
+Support for processing data in so-called “colorspace”, as produced by
+the ABI SOLiD sequencer, was removed from Cutadapt versions newer than
+1.18.
 
-    cutadapt -c --format=sra-fastq -a CGCCTTGGCCG sra.fastq > trimmed.fastq
+To process colorspace data, please use Cutadapt 1.18 or earlier.
+That version also knows how to process ``.csfasta``/``.qual`` file
+pairs.
 
-When you use ``--format=sra-fastq``, the spurious quality value will be removed
-from all reads in the file.
+`See also the colorspace section in the documentation for
+Cutadapt 1.18 <https://cutadapt.readthedocs.io/en/v1.18/colorspace.html>`_.

doc/conf.py

@@ -47,22 +47,20 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'cutadapt'
-copyright = u'2010-2018, Marcel Martin'
+copyright = u'2010-2019, Marcel Martin'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-from cutadapt import __version__
-# The short X.Y version.
-version = __version__
-
+from pkg_resources import get_distribution
+release = get_distribution('cutadapt').version
 # Read The Docs modifies the conf.py script and we therefore get
-# version numbers like 0.7+0.g27d0d31.dirty from versioneer.
-if version.endswith('.dirty') and os.environ.get('READTHEDOCS') == 'True':
-	version, _, rest = version.partition('+')
-	if not rest.startswith('0.'):
-		version = version + '+' + rest[:-6]
+# version numbers like 0.12+0.g27d0d31
+if os.environ.get('READTHEDOCS') == 'True':
+    version = '.'.join(release.split('.')[:2])
+else:
+    version = release
 
 # The full version, including alpha/beta/rc tags.
 release = version

doc/develop.rst

@@ -2,9 +2,8 @@ Developing
 ==========
 
 The `Cutadapt source code is on GitHub <https://github.com/marcelm/cutadapt/>`_.
-Cutadapt is written in Python with some extension modules that are written
-in Cython. Cutadapt uses a single code base that is compatible with both
-Python 2 and 3. Python 2.7 is the minimum supported Python version.
+Cutadapt is written in Python 3 with some extension modules that are written
+in Cython. Support for Python 2 has been dropped.
 
 
 Development installation
@@ -15,8 +14,8 @@ using a virtualenv. This sequence of commands should work::
 
     git clone https://github.com/marcelm/cutadapt.git  # or clone your own fork
     cd cutadapt
-	virtualenv -p python3 venv  # or omit the "-p python3" for Python 2
-	venv/bin/pip3 install Cython pytest nose tox  # pip3 becomes just pip for Python 2
+    python3 -m venv venv
+    venv/bin/pip3 install Cython pytest nose tox
     venv/bin/pip3 install -e .
 
 Then you can run Cutadapt like this (or activate the virtualenv and omit the
@@ -40,7 +39,7 @@ Development installation (without virtualenv)
 Alternatively, if you do not want to use virtualenv, running the following may
 work from within the cloned repository::
 
-	python3 setup.py build_ext -i  # omit the "3" for Python 2
+    python3 setup.py build_ext -i
     pytest
 
 This requires Cython and pytest to be installed. Avoid this method and use a

doc/ideas.rst

@@ -6,24 +6,17 @@ things that could be improved in the source code, and of possible algorithmic
 improvements.
 
 - show average error rate
-- In colorspace and probably also for Illumina data, gapped alignment
-  is not necessary
-- ``--progress``
 - run pylint, pychecker
 - length histogram
-- check whether input is FASTQ although -f fasta is given
 - search for adapters in the order in which they are given on the
   command line
 - more tests for the alignment algorithm
 - ``--detect`` prints out best guess which of the given adapters is the correct one
-- alignment algorithm: make a 'banded' version
 - it seems the str.find optimization isn't very helpful. In any case, it should be
   moved into the Aligner class.
 - allow to remove not the adapter itself, but the sequence before or after it
-- instead of trimming, convert adapter to lowercase
 - warn when given adapter sequence contains non-IUPAC characters
 - extensible file type detection
-- the --times setting should be an attribute of Adapter
 
 
 Backwards-incompatible changes
@@ -31,7 +24,6 @@ Backwards-incompatible changes
 
 - Drop ``--rest-file`` support
 - Possibly drop wildcard-file support, extend info-file instead
-- Drop "legacy mode"
 - For non-anchored 5' adapters, find rightmost match
 
 
@@ -87,16 +79,6 @@ Model somehow all the flags that exist for semiglobal alignment. For start of th
 Not degraded and no bases before allowed = anchored.
 Degraded and bases before allowed = regular 5'
 
-By default, the 5' end should be anchored, the 3' end not.
-
-* ``-a ADAPTER...`` → not degraded, no bases before allowed
-* ``-a N*ADAPTER...`` → not degraded, bases before allowed
-* ``-a ADAPTER^...`` → degraded, no bases before allowed
-* ``-a N*ADAPTER^...`` → degraded, bases before allowed
-* ``-a ...ADAPTER`` → degraded, bases after allowed
-* ``-a ...ADAPTER$`` → not degraded, no bases after allowed
-
-
 
 Paired-end trimming
 -------------------
@@ -108,4 +90,4 @@ Available/used letters for command-line options
 
 * Remaining characters: All uppercase letters except A, B, G, M, N, O, U
 * Lowercase letters: i, j, k, s, w
-* Planned/reserved: Q (paired-end quality trimming), j (multithreading)
+* Planned/reserved: Q (paired-end quality trimming)

doc/installation.rst

@@ -9,14 +9,14 @@ successfully under macOS and Windows.
 Quick installation
 ------------------
 
-The easiest way to install cutadapt is to use ``pip`` on the command line::
+The easiest way to install Cutadapt is to use ``pip3`` on the command line::
 
-    pip install --user --upgrade cutadapt
+    pip3 install --user --upgrade cutadapt
 
 This will download the software from `PyPI (the Python packaging
 index) <https://pypi.python.org/pypi/cutadapt/>`_, and
 install the cutadapt binary into ``$HOME/.local/bin``. If an old version of
-cutadapt exists on your system, the ``--upgrade`` parameter is required in order
+Cutadapt exists on your system, the ``--upgrade`` parameter is required in order
 to install a newer version. You can then run the program like this::
 
     ~/.local/bin/cutadapt --help
@@ -28,14 +28,14 @@ If you want to avoid typing the full path, add the directory
 Installation with conda
 -----------------------
 
-Alternatively, cutadapt is available as a conda package from the
+Alternatively, Cutadapt is available as a conda package from the
 `bioconda channel <https://bioconda.github.io/>`_. If you do not have conda,
 `install miniconda <http://conda.pydata.org/miniconda.html>`_ first.
-Then install cutadapt like this::
+Then install Cutadapt like this::
 
     conda install -c bioconda cutadapt
 
-If neither `pip` nor `conda` installation works, keep reading.
+If neither ``pip`` nor ``conda`` installation works, keep reading.
 
 
 .. _dependencies:
@@ -45,37 +45,44 @@ Dependencies
 
 Cutadapt installation requires this software to be installed:
 
-* Python 2.7 or at least Python 3.4
-* Possibly a C compiler. For Linux, cutadapt packages are provided as
+* Python 3.4 or newer
+* Possibly a C compiler. For Linux, Cutadapt packages are provided as
   so-called “wheels” (``.whl`` files) which come pre-compiled.
 
 Under Ubuntu, you may need to install the packages ``build-essential`` and
-``python-dev`` (or ``python3-dev``) to get a C compiler.
-
-On Windows, you need `Microsoft Visual C++ Compiler for
-Python 2.7 <https://www.microsoft.com/en-us/download/details.aspx?id=44266>`_.
+``python3-dev`` to get a C compiler.
 
 If you get an error message::
 
     error: command 'gcc' failed with exit status 1
 
 Then check the entire error message. If it says something about a missing
-``Python.h`` file, then the problem are missing Python development
-packages (``python-dev``/``python3-dev`` in Ubuntu).
+``Python.h`` file, then the problem is that you are missing Python development
+packages (``python3-dev`` in Ubuntu).
 
 
 System-wide installation (root required)
 ----------------------------------------
 
-If you have root access, then you can install cutadapt system-wide by running::
+If you have root access, then you can install Cutadapt system-wide by running::
 
-    sudo pip install cutadapt
+    sudo python3 -m pip install cutadapt
 
-This installs cutadapt into `/usr/local/bin`.
+This installs cutadapt into ``/usr/local/bin``.
 
 If you want to upgrade from an older version, use this command instead::
 
-    sudo pip install --upgrade cutadapt
+    sudo python3 -m pip install --upgrade cutadapt
+
+
+If the above does not work for you, then you can try to install Cutadapt
+into a virtual environment. This may lead to fewer conflicts with
+system-installed packages::
+
+    sudo python3 -m venv /usr/local/cutadapt
+    sudo /usr/local/cutadapt/bin/pip install cutadapt
+    cd /usr/local/bin/
+    sudo ln -s ../cutadapt/bin/cutadapt
 
 
 Uninstalling
@@ -83,7 +90,7 @@ Uninstalling
 
 Type  ::
 
-    pip uninstall cutadapt
+    pip3 uninstall cutadapt
 
 and confirm with ``y`` to remove the package. Under some circumstances, multiple
 versions may be installed at the same time. Repeat the above command until you
@@ -93,7 +100,7 @@ get an error message in order to make sure that all versions are removed.
 Shared installation (on a cluster)
 ----------------------------------
 
-If you have a larger installation and want to provide cutadapt as a module
+If you have a larger installation and want to provide Cutadapt as a module
 that can be loaded and unloaded (with the Lmod system, for example), we
 recommend that you create a virtual environment and 'pip install' cutadapt into
 it. These instructions work on our SLURM cluster that uses the Lmod system
@@ -105,7 +112,7 @@ it. These instructions work on our SLURM cluster that uses the Lmod system
 
 The ``install-option`` part is important. It ensures that a second, separate
 ``bin/`` directory is created (``/software/cutadapt-1.9.1/bin/``) that *only*
-contains the ``cutadapt`` script and nothing else. To make cutadapt available to
+contains the ``cutadapt`` script and nothing else. To make Cutadapt available to
 the users, that directory (``$BASE/bin``) needs to be added to the ``$PATH``.
 
 Make sure you *do not* add the ``bin/`` directory within the ``venv`` directory
@@ -128,11 +135,11 @@ Activation merely adds the ``bin/`` directory to the ``$PATH``, so the
 Installing the development version
 ----------------------------------
 
-We recommend that you install cutadapt into a so-called virtual environment if
+We recommend that you install Cutadapt into a so-called virtual environment if
 you decide to use the development version. The virtual environment is a single
 directory that contains everything needed to run the software. Nothing else on
 your system is changed, so you can simply uninstall this particular version of
-cutadapt by removing the directory with the virtual environment.
+Cutadapt by removing the directory with the virtual environment.
 
 The following instructions work on Linux using Python 3. Make sure you have
 installed the :ref:`dependencies <dependencies>` (``python3-dev`` and
@@ -143,13 +150,13 @@ environment and what you want to call it. Let us assume you chose the path
 ``~/cutadapt-venv``. Then use these commands for the installation::
 
     python3 -m venv ~/cutadapt-venv
-    ~/cutadapt-venv/bin/pip install Cython
-    ~/cutadapt-venv/bin/pip install https://github.com/marcelm/cutadapt/archive/master.zip
+    ~/cutadapt-venv/bin/python3 -m pip install --upgrade pip
+    ~/cutadapt-venv/bin/pip install git+https://github.com/marcelm/cutadapt.git#egg=cutadapt
 
-To run cutadapt and see the version number, type ::
+To run Cutadapt and see the version number, type ::
 
     ~/cutadapt-venv/bin/cutadapt --version
 
-The reported version number will be something like ``1.14+65.g5610275``. This
-means that you are now running a cutadapt version that contains 65 additional
-changes (*commits*) since version 1.14.
+The reported version number will be something like ``2.2.dev5+gf564208``. This
+means that you are now running the version of Cutadapt that will become 2.2, and that is contains
+5 changes (*commits*) since the previous release (2.1 in this case).

doc/recipes.rst

-=============
-Recipes (FAQ)
-=============
+===============
+Recipes and FAQ
+===============
 
 This section gives answers to frequently asked questions. It shows you how to
-get cutadapt to do what you want it to do!
+get Cutadapt to do what you want it to do!
 
 
 Remove more than one adapter
@@ -20,13 +20,13 @@ version ``-n 2``). For example::
 
     cutadapt -g ^TTAAGGCC -g ^AAGCTTA -a TACGGACT -n 2 -o output.fastq input.fastq
 
-This instructs cutadapt to run two rounds of adapter finding and removal. That
+This instructs Cutadapt to run two rounds of adapter finding and removal. That
 means that, after the first round and only when an adapter was actually found,
 another round is performed. In both rounds, all given adapters are searched and
 removed. The problem is that it could happen that one adapter is found twice (so
 the 3' adapter, for example, could be removed twice).
 
-The second option is to not use the ``-n`` option, but to run cutadapt twice,
+The second option is to not use the ``-n`` option, but to run Cutadapt twice,
 first removing one adapter and then the other. It is easiest if you use a pipe
 as in this example::
 
@@ -38,7 +38,7 @@ Trim poly-A tails
 
 If you want to trim a poly-A tail from the 3' end of your reads, use the 3'
 adapter type (``-a``) with an adapter sequence of many repeated ``A``
-nucleotides. Starting with version 1.8 of cutadapt, you can use the
+nucleotides. Starting with version 1.8 of Cutadapt, you can use the
 following notation to specify a sequence that consists of 100 ``A``::
 
     cutadapt -a "A{100}" -o output.fastq input.fastq
@@ -54,7 +54,7 @@ will be trimmed to::
 
 If for some reason you would like to use a shorter sequence of ``A``, you can
 do so: The matching algorithm always picks the leftmost match that it can find,
-so cutadapt will do the right thing even when the tail has more ``A`` than you
+so Cutadapt will do the right thing even when the tail has more ``A`` than you
 used in the adapter sequence. However, sequencing errors may result in shorter
 matches than desired. For example, using ``-a "A{10}"``, the read above (where
 the ``AAAT`` is followed by eleven ``A``) would be trimmed to::
@@ -114,7 +114,7 @@ the linked adapter option that needs to be used is therefore ::
 where ``FWDPRIMER`` needs to be replaced with the sequence of your
 forward primer and ``RCREVPRIMER`` with the reverse complement of
 the reverse primer. The three dots ``...`` need to be entered
-as they are -- they tell cutadapt that this is a linked adapter
+as they are -- they tell Cutadapt that this is a linked adapter
 with a 5' and a 3' part.
 
 Sequencing of R2 starts before the 3' sequencing primer and
@@ -127,7 +127,7 @@ swapped and reverse-complemented::
 The uppercase ``-A`` specifies that this option is
 meant to work on R2. Similar to above, ``REVPRIMER`` is
 the sequence of the reverse primer and ``RCFWDPRIMER`` is the
-reverse-complement of the forward primer. Note that cutadapt
+reverse-complement of the forward primer. Note that Cutadapt
 does not reverse-complement any sequences of its own; you
 will have to do that yourself.
 
@@ -158,7 +158,7 @@ you know must be there::
 Piping paired-end data
 ----------------------
 
-Sometimes it is necessary to run cutadapt twice on your data. For example, when
+Sometimes it is necessary to run Cutadapt twice on your data. For example, when
 you want to change the order in which read modification or filtering options are
 applied. To simplify this, you can use Unix pipes (``|``), but this is more
 difficult with paired-end data since then input and output consists of two files
@@ -171,13 +171,113 @@ principle::
     cutadapt [options] --interleaved in.1.fastq.gz in.2.fastq.gz | \
       cutadapt [options] --interleaved -o out.1.fastq.gz -p out.2.fastq.gz -
 
-Note the ``-`` character in the second invocation to cutadapt.
+Note the ``-`` character in the second invocation to Cutadapt.
+
+
+Support for concatenated compressed files
+-----------------------------------------
+
+Cutadapt supports concatenated gzip and bzip2 input files.
+
+
+Paired-end read name check
+--------------------------
+
+When reading paired-end files, Cutadapt checks whether the read names match.
+Only the part of the read name before the first space is considered. If the
+read name ends with ``1`` or ``2``, then that is also ignored. For example,
+two FASTQ headers that would be considered to denote properly paired reads are::
+
+    @my_read/1 a comment
+
+and::
+
+    @my_read/2 another comment
+
+This is an example for *improperly paired* read names::
+
+    @my_read/1;1
+
+and::
+
+    @my_read/2;1
+
+Since the ``1`` and ``2`` are ignored only if the occur at the end of the read
+name, and since the ``;1`` is considered to be part of the read name, these
+reads will not be considered to be propely paired.
+
+
+Rescuing single reads from paired-end reads that were filtered
+--------------------------------------------------------------
+
+When trimming and filtering paired-end reads, Cutadapt always discards entire read pairs. If you
+want to keep one of the reads, you need to write the filtered read pairs to an output file and
+postprocess it.
+
+For example, assume you are using ``-m 30`` to discard too short reads. Cutadapt discards all
+read pairs in which just one of the reads is too short (but see the ``--pair-filter`` option).
+To recover those (individual) reads that are long enough, you can first use the
+``--too-short-(paired)-output`` options to write the filtered pairs to a file, and then postprocess
+those files to keep only the long enough reads.
+
+
+    cutadapt -m 30 -q 20 -o out.1.fastq.gz -p out.2.fastq.gz --too-short-output=tooshort.1.fastq.gz --too-short-paired-output=tooshort.2.fastq.gz in.1.fastq.gz in.2.fastq.gz
+    cutadapt -m 30 -o rescued.a.fastq.gz tooshort.1.fastq.gz
+    cutadapt -m 30 -o rescued.b.fastq.gz tooshort.2.fastq.gz
+
+The two output files ``rescued.a.fastq.gz`` and ``rescued.b.fastq.gz`` contain those individual
+reads that are long enough. Note that the file names do not end in ``.1.fastq.gz`` and
+``.2.fastq.gz`` to make it very clear that these files no longer contain synchronized paired-end
+reads.
+
+
+.. _bisulfite:
+
+Bisulfite sequencing (RRBS)
+---------------------------
+
+When trimming reads that come from a library prepared with the RRBS (reduced
+representation bisulfite sequencing) protocol, the last two 3' bases must be
+removed in addition to the adapter itself. This can be achieved by using not
+the adapter sequence itself, but by adding two wildcard characters to its
+beginning. If the adapter sequence is ``ADAPTER``, the command for trimming
+should be::
+
+    cutadapt -a NNADAPTER -o output.fastq input.fastq
+
+Details can be found in `Babraham bioinformatics' "Brief guide to
+RRBS" <http://www.bioinformatics.babraham.ac.uk/projects/bismark/RRBS_Guide.pdf>`_.
+A summary follows.
+
+During RRBS library preparation, DNA is digested with the restriction enzyme
+MspI, generating a two-base overhang on the 5' end (``CG``). MspI recognizes
+the sequence ``CCGG`` and cuts
+between ``C`` and ``CGG``. A double-stranded DNA fragment is cut in this way::
+
+    5'-NNNC|CGGNNN-3'
+    3'-NNNGGC|CNNN-5'
+
+The fragment between two MspI restriction sites looks like this::
+
+    5'-CGGNNN...NNNC-3'
+      3'-CNNN...NNNGGC-5'
+
+Before sequencing (or PCR) adapters can be ligated, the missing base positions
+must be filled in with GTP and CTP::
+
+    5'-ADAPTER-CGGNNN...NNNCcg-ADAPTER-3'
+    3'-ADAPTER-gcCNNN...NNNGGC-ADAPTER-5'
+
+The filled-in bases, marked in lowercase above, do not contain any original
+methylation information, and must therefore not be used for methylation calling.
+By prefixing the adapter sequence with ``NN``, the bases will be automatically
+stripped during adapter trimming.
 
 
 Other things (unfinished)
 -------------------------
 
 * How to detect adapters
-* Use cutadapt for quality-trimming only
+* Use Cutadapt for quality-trimming only
 * Use it for minimum/maximum length filtering
 * Use it for conversion to FASTQ

pyproject.toml

+[build-system]
+requires = ["setuptools", "wheel", "setuptools_scm", "cython"]

setup.cfg

-[versioneer]
-vcs = git
-style = pep440
-versionfile_source = src/cutadapt/_version.py
-versionfile_build = cutadapt/_version.py
-tag_prefix = v
-parentdir_prefix = cutadapt-
-
-[egg_info]
-tag_build = 
-tag_date = 0
-

setup.py

 """
-Build cutadapt.
+Build Cutadapt.
 """
 import sys
 import os.path
@@ -8,13 +8,11 @@ from setuptools import setup, Extension, find_packages
 from distutils.version import LooseVersion
 from distutils.command.sdist import sdist as _sdist
 from distutils.command.build_ext import build_ext as _build_ext
-import versioneer
 
-MIN_CYTHON_VERSION = '0.24'
+MIN_CYTHON_VERSION = '0.28'
 
-vi = sys.version_info
-if (vi[0] == 2 and vi[1] < 7) or (vi[0] == 3 and vi[1] < 4):
-	sys.stdout.write('Minimum supported Python versions are 2.7 and 3.4.\n')
+if sys.version_info[:2] < (3, 4):
+    sys.stdout.write('You need at least Python 3.4\n')
     sys.exit(1)
 
 
@@ -56,16 +54,11 @@ def check_cython_version():
 
 extensions = [
     Extension('cutadapt._align', sources=['src/cutadapt/_align.pyx']),
-	Extension('cutadapt._qualtrim', sources=['src/cutadapt/_qualtrim.pyx']),
-	Extension('cutadapt._seqio', sources=['src/cutadapt/_seqio.pyx']),
+    Extension('cutadapt.qualtrim', sources=['src/cutadapt/qualtrim.pyx']),
 ]
 
-cmdclass = versioneer.get_cmdclass()
-versioneer_build_ext = cmdclass.get('build_ext', _build_ext)
-versioneer_sdist = cmdclass.get('sdist', _sdist)
 
-
-class build_ext(versioneer_build_ext):
+class BuildExt(_build_ext):
     def run(self):
         # If we encounter a PKG-INFO file, then this is likely a .tar.gz/.zip
         # file retrieved from PyPI that already includes the pre-cythonized
@@ -78,20 +71,16 @@ class build_ext(versioneer_build_ext):
             check_cython_version()
             from Cython.Build import cythonize
             self.extensions = cythonize(self.extensions)
-		versioneer_build_ext.run(self)
+        super().run()
 
 
-class sdist(versioneer_sdist):
+class SDist(_sdist):
     def run(self):
         # Make sure the compiled Cython files in the distribution are up-to-date
         from Cython.Build import cythonize
         check_cython_version()
         cythonize(extensions)
-		versioneer_sdist.run(self)
-
-
-cmdclass['build_ext'] = build_ext
-cmdclass['sdist'] = sdist
+        super().run()
 
 
 encoding_arg = {'encoding': 'utf-8'} if sys.version > '3' else dict()
@@ -100,22 +89,24 @@ with open('README.rst', **encoding_arg) as f:
 
 setup(
     name='cutadapt',
-	version=versioneer.get_version(),
+    setup_requires=['setuptools_scm'],  # Support pip versions that don't know about pyproject.toml
+    use_scm_version={'write_to': 'src/cutadapt/_version.py'},
     author='Marcel Martin',
     author_email='marcel.martin@scilifelab.se',
     url='https://cutadapt.readthedocs.io/',
     description='trim adapters from high-throughput sequencing reads',
     long_description=long_description,
     license='MIT',
-	cmdclass=cmdclass,
+    cmdclass={'build_ext': BuildExt, 'sdist': SDist},
     ext_modules=extensions,
     package_dir={'': 'src'},
     packages=find_packages('src'),
     entry_points={'console_scripts': ['cutadapt = cutadapt.__main__:main']},
-	install_requires=['xopen>=0.3.2'],
+    install_requires=['dnaio>=0.3', 'xopen>=0.5.0'],
     extras_require={
-		'dev': ['Cython', 'pytest', 'pytest-timeout', 'nose', 'sphinx', 'sphinx_issues'],
+        'dev': ['Cython', 'pytest', 'pytest-timeout', 'sphinx', 'sphinx_issues'],
     },
+    python_requires='>=3.4',
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Environment :: Console",
@@ -123,8 +114,7 @@ setup(
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Programming Language :: Cython",
-		"Programming Language :: Python :: 2.7",
         "Programming Language :: Python :: 3",
         "Topic :: Scientific/Engineering :: Bio-Informatics"
-	]
+    ],
 )

src/cutadapt.egg-info/PKG-INFO

-Metadata-Version: 1.1
-Name: cutadapt
-Version: 1.18
-Summary: trim adapters from high-throughput sequencing reads
-Home-page: https://cutadapt.readthedocs.io/
-Author: Marcel Martin
-Author-email: marcel.martin@scilifelab.se
-License: MIT
-Description-Content-Type: UNKNOWN
-Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master
-            :target: https://travis-ci.org/marcelm/cutadapt
-        
-        .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master
-            :target: https://pypi.python.org/pypi/cutadapt
-        
-        ========
-        cutadapt
-        ========
-        
-        Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
-        types of unwanted sequence from your high-throughput sequencing reads.
-        
-        Cleaning your data in this way is often required: Reads from small-RNA
-        sequencing contain the 3’ sequencing adapter because the read is longer than
-        the molecule that is sequenced. Amplicon reads start with a primer sequence.
-        Poly-A tails are useful for pulling out RNA from your sample, but often you
-        don’t want them to be in your reads.
-        
-        Cutadapt helps with these trimming tasks by finding the adapter or primer
-        sequences in an error-tolerant way. It can also modify and filter reads in
-        various ways. Adapter sequences can contain IUPAC wildcard characters. Also,
-        paired-end reads and even colorspace data is supported. If you want, you can
-        also just demultiplex your input data, without removing adapter sequences at all.
-        
-        Cutadapt comes with an extensive suite of automated tests and is available under
-        the terms of the MIT license.
-        
-        If you use cutadapt, please cite
-        `DOI:10.14806/ej.17.1.200 <http://dx.doi.org/10.14806/ej.17.1.200>`_ .
-        
-        
-        Links
-        -----
-        
-        * `Documentation <https://cutadapt.readthedocs.io/>`_
-        * `Source code <https://github.com/marcelm/cutadapt/>`_
-        * `Report an issue <https://github.com/marcelm/cutadapt/issues>`_
-        * `Project page on PyPI (Python package index) <https://pypi.python.org/pypi/cutadapt/>`_
-        * `Follow @marcelm_ on Twitter <https://twitter.com/marcelm_>`_
-        * `Wrapper for the Galaxy platform <https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper>`_
-        
-Platform: UNKNOWN
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Natural Language :: English
-Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

src/cutadapt.egg-info/SOURCES.txt

-CHANGES.rst
-CITATION
-LICENSE
-MANIFEST.in
-README.rst
-setup.cfg
-setup.py
-versioneer.py
-doc/Makefile
-doc/algorithms.rst
-doc/changes.rst
-doc/colorspace.rst
-doc/conf.py
-doc/develop.rst
-doc/guide.rst
-doc/ideas.rst
-doc/index.rst
-doc/installation.rst
-doc/recipes.rst
-src/cutadapt/__init__.py
-src/cutadapt/__main__.py
-src/cutadapt/_align.c
-src/cutadapt/_align.pyx
-src/cutadapt/_qualtrim.c
-src/cutadapt/_qualtrim.pyx
-src/cutadapt/_seqio.c
-src/cutadapt/_seqio.pyx
-src/cutadapt/_version.py
-src/cutadapt/adapters.py
-src/cutadapt/align.py
-src/cutadapt/colorspace.py
-src/cutadapt/compat.py
-src/cutadapt/filters.py
-src/cutadapt/modifiers.py
-src/cutadapt/pipeline.py
-src/cutadapt/qualtrim.py
-src/cutadapt/report.py
-src/cutadapt/seqio.py
-src/cutadapt/utils.py
-src/cutadapt.egg-info/PKG-INFO
-src/cutadapt.egg-info/SOURCES.txt
-src/cutadapt.egg-info/dependency_links.txt
-src/cutadapt.egg-info/entry_points.txt
-src/cutadapt.egg-info/requires.txt
-src/cutadapt.egg-info/top_level.txt
-tests/test_adapters.py
-tests/test_align.py
-tests/test_colorspace.py
-tests/test_commandline.py
-tests/test_filters.py
-tests/test_modifiers.py
-tests/test_paired.py
-tests/test_qualtrim.py
-tests/test_seqio.py
-tests/test_trim.py
-tests/utils.py
-tests/cut/454.fa
-tests/cut/SRR2040271_1.fastq
-tests/cut/adapterx.fasta
-tests/cut/anchored-back.fasta
-tests/cut/anchored.fasta
-tests/cut/anchored_no_indels.fasta
-tests/cut/anchored_no_indels_wildcard.fasta
-tests/cut/anywhere_repeat.fastq
-tests/cut/casava.fastq
-tests/cut/demultiplexed.first.1.fastq
-tests/cut/demultiplexed.first.2.fastq
-tests/cut/demultiplexed.second.1.fastq
-tests/cut/demultiplexed.second.2.fastq
-tests/cut/demultiplexed.unknown.1.fastq
-tests/cut/demultiplexed.unknown.2.fastq
-tests/cut/discard-untrimmed.fastq
-tests/cut/discard.fastq
-tests/cut/dos.fastq
-tests/cut/empty.fastq
-tests/cut/example.fa
-tests/cut/examplefront.fa
-tests/cut/illumina.fastq
-tests/cut/illumina.info.txt
-tests/cut/illumina5.fastq
-tests/cut/illumina5.info.txt
-tests/cut/illumina64.fastq
-tests/cut/interleaved.fastq
-tests/cut/issue46.fasta
-tests/cut/linked-anchored.fasta
-tests/cut/linked-discard-g.fasta
-tests/cut/linked-discard.fasta
-tests/cut/linked-not-anchored.fasta
-tests/cut/linked.fasta
-tests/cut/lowercase.fastq
-tests/cut/lowqual.fastq
-tests/cut/maxlen.fa
-tests/cut/maxn0.2.fasta
-tests/cut/maxn0.4.fasta
-tests/cut/maxn0.fasta
-tests/cut/maxn1.fasta
-tests/cut/maxn2.fasta
-tests/cut/minlen.fa
-tests/cut/minlen.noprimer.fa
-tests/cut/nextseq.fastq
-tests/cut/no-trim.fastq
-tests/cut/no_indels.fasta
-tests/cut/overlapa.fa
-tests/cut/overlapb.fa
-tests/cut/paired-filterboth.1.fastq
-tests/cut/paired-filterboth.2.fastq
-tests/cut/paired-filterfirst.1.fastq
-tests/cut/paired-filterfirst.2.fastq
-tests/cut/paired-m27.1.fastq
-tests/cut/paired-m27.2.fastq
-tests/cut/paired-onlyA.1.fastq
-tests/cut/paired-onlyA.2.fastq
-tests/cut/paired-separate.1.fastq
-tests/cut/paired-separate.2.fastq
-tests/cut/paired-too-short.1.fastq
-tests/cut/paired-too-short.2.fastq
-tests/cut/paired-trimmed.1.fastq
-tests/cut/paired-trimmed.2.fastq
-tests/cut/paired-untrimmed.1.fastq
-tests/cut/paired-untrimmed.2.fastq
-tests/cut/paired.1.fastq
-tests/cut/paired.2.fastq
-tests/cut/paired.m14.1.fastq
-tests/cut/paired.m14.2.fastq
-tests/cut/pairedq.1.fastq
-tests/cut/pairedq.2.fastq
-tests/cut/pairedu.1.fastq
-tests/cut/pairedu.2.fastq
-tests/cut/plus.fastq
-tests/cut/polya.fasta
-tests/cut/rest.fa
-tests/cut/restfront.fa
-tests/cut/s_1_sequence.txt
-tests/cut/shortened-negative.fastq
-tests/cut/shortened.fastq
-tests/cut/small-no-trim.fasta
-tests/cut/small.fasta
-tests/cut/small.fastq
-tests/cut/small.trimmed.fastq
-tests/cut/small.untrimmed.fastq
-tests/cut/solid-no-zerocap.fastq
-tests/cut/solid.fasta
-tests/cut/solid.fastq
-tests/cut/solid5p-anchored.fasta
-tests/cut/solid5p-anchored.fastq
-tests/cut/solid5p-anchored.notrim.fasta
-tests/cut/solid5p-anchored.notrim.fastq
-tests/cut/solid5p.fasta
-tests/cut/solid5p.fastq
-tests/cut/solidbfast.fastq
-tests/cut/solidmaq.fastq
-tests/cut/solidqual.fastq
-tests/cut/sra.fastq
-tests/cut/stripped.fasta
-tests/cut/suffix.fastq
-tests/cut/trimN3.fasta
-tests/cut/trimN5.fasta
-tests/cut/twoadapters.fasta
-tests/cut/twoadapters.first.fasta
-tests/cut/twoadapters.second.fasta
-tests/cut/twoadapters.unknown.fasta
-tests/cut/unconditional-back.fastq
-tests/cut/unconditional-both.fastq
-tests/cut/unconditional-front.fastq
-tests/cut/wildcard.fa
-tests/cut/wildcardN.fa
-tests/cut/wildcard_adapter.fa
-tests/cut/wildcard_adapter_anywhere.fa
-tests/cut/xadapter.fasta
-tests/data/454.fa
-tests/data/E3M.fasta
-tests/data/E3M.qual
-tests/data/SRR2040271_1.fastq
-tests/data/adapter.fasta
-tests/data/anchored-back.fasta
-tests/data/anchored.fasta
-tests/data/anchored_no_indels.fasta
-tests/data/anywhere_repeat.fastq
-tests/data/casava.fastq
-tests/data/dos.fastq
-tests/data/empty.fastq
-tests/data/example.fa
-tests/data/illumina.fastq.gz
-tests/data/illumina5.fastq
-tests/data/illumina64.fastq
-tests/data/interleaved.fastq
-tests/data/issue46.fasta
-tests/data/lengths.fa
-tests/data/linked.fasta
-tests/data/lowqual.fastq
-tests/data/maxn.fasta
-tests/data/multiblock.fastq.bz2
-tests/data/multiblock.fastq.gz
-tests/data/nextseq.fastq
-tests/data/no_indels.fasta
-tests/data/overlapa.fa
-tests/data/overlapb.fa
-tests/data/paired.1.fastq
-tests/data/paired.2.fastq
-tests/data/plus.fastq
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-tests/data/rest.fa
-tests/data/rest.txt
-tests/data/restfront.txt
-tests/data/s_1_sequence.txt.gz
-tests/data/simple.fasta
-tests/data/simple.fastq
-tests/data/small.fastq
-tests/data/small.fastq.bz2
-tests/data/small.fastq.gz
-tests/data/small.fastq.xz
-tests/data/small.myownextension
-tests/data/solid.csfasta
-tests/data/solid.fasta
-tests/data/solid.fastq
-tests/data/solid.qual
-tests/data/solid5p.fasta
-tests/data/solid5p.fastq
-tests/data/sra.fastq
-tests/data/suffix-adapter.fasta
-tests/data/toolong.fa
-tests/data/tooshort.fa
-tests/data/tooshort.noprimer.fa
-tests/data/trimN3.fasta
-tests/data/trimN5.fasta
-tests/data/twoadapters.fasta
-tests/data/underscore_fastq.gz
-tests/data/wildcard.fa
-tests/data/wildcardN.fa
-tests/data/wildcard_adapter.fa
-tests/data/withplus.fastq
-tests/data/xadapterx.fasta
\ No newline at end of file

src/cutadapt.egg-info/dependency_links.txt

-