.codecov.yml

+comment: off
+
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  precision: 1
+  round: down
+  range: "90...100"
+
+  status:
+    project: yes
+    patch: no
+    changes: no
+
+comment: off

.editorconfig

+[*.{py,pyx,rst}]
+charset=utf-8
+end_of_line=lf
+insert_final_newline=true
+indent_style=space
+indent_size=4

.github/issue_template.md

+<!--
+When reporting an issue, please include this information:
+
+- Cutadapt and Python version
+- How you installed the tool (conda or pip, for example)
+- Which command-line parameters you used
+
+If you report unexpected trimming behavior, this would also be helpful:
+
+- An example input read (or read pair)
+- The output that cutadapt produces
+- The output that you would have expected
+
+Feel free to delete this text before submitting your issue.
+-->

.gitignore

+# Editor-specific ignore patterns such as "*~" should be added to
+# ~/.config/git/ignore, not here.
+
+*.pyc
+__pycache__/
+/MANIFEST
+/build/
+/dist/
+/.coverage
+/.tox
+/.cache
+/.pytest_cache
+/src/cutadapt/*.c
+/src/cutadapt/*.so
+/doc/_build
+/src/cutadapt.egg-info/
+src/cutadapt/_version.py

.travis.yml

+language: python
+
+dist: xenial
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+
+python:
+  - "3.5"
+  - "3.6"
+  - "3.7"
+  - "3.8-dev"
+  - "nightly"
+
+install:
+  - pip install 'Cython>=0.28' tox-travis
+
+script:
+  - tox
+
+after_success:
+  - pip install codecov
+  - codecov
+
+env:
+  global:
+    #- TWINE_REPOSITORY_URL=https://test.pypi.org/legacy/
+    - TWINE_USERNAME=marcelm
+    # TWINE_PASSWORD is set in Travis settings
+
+jobs:
+  include:
+    - stage: deploy
+      services:
+        - docker
+      python: "3.6"
+      install: python3 -m pip install Cython twine
+      if: tag IS present
+      script:
+        - |
+          python3 setup.py sdist
+          ./buildwheels.sh
+          ls -l dist/
+          python3 -m twine upload dist/*
+
+    - name: flake8
+      python: "3.6"
+      install: python3 -m pip install flake8
+      script: flake8 src/ tests/
+
+  allow_failures:
+    - python: "nightly"

CHANGES.rst

@@ -2,6 +2,19 @@
 Changes
 =======
 
+v2.6 (2019-10-26)
+-----------------
+
+* :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).
+
+
 v2.5 (2019-09-04)
 -----------------
 

CONTRIBUTING.rst

+Contributing
+------------
+
+Contributions to Cutadapt in the form of source code or documentation
+improvements or helping out with responding to issues are welcome!
+
+To contribute to Cutadapt development, it is easiest to send in a pull request
+(PR) on GitHub.
+
+Here are some guidelines for how to do this. They are not strict rules. When in
+doubt, send in a PR and we will sort it out.
+
+* Limit a PR to a single topic. Submit multiple PRs if necessary. This way, it
+  is easier to discuss the changes individually, and in case we find that one
+  of them should not go in, the others can still be accepted.
+* For larger changes, consider opening an issue first to plan what you want to
+  do.
+* Include appropriate unit or integration tests. Sometimes, tests are hard to
+  write or don’t make sense. If you think this is the case, just leave the tests
+  out initially and we can discuss whether to add any.
+* Add documentation and a changelog entry if appropriate.
+
+
+Code style
+~~~~~~~~~~
+
+* Cutadapt tries to follow PEP8, except that the allowed line length is 100
+  characters, not 80. But try to wrap comments after 80 characters.
+* There are inconsistencies in the current code base since it’s a few years old
+  already. New code should follow the current rules, however.
+* At the moment, no automatic code formatting is done, but one idea might be to
+  switch to the `black <https://black.readthedocs.io/>`_ code formatter at some
+  point. If you’re familiar with its style, you can use that already now for
+  new code to make the diff smaller.
+* Prefer double quotation marks in new code. This will also make the diff smaller
+  if we eventually switch to black.
+* Using an IDE is beneficial (PyCharm, for example). It helps to catch lots of
+  style issues early (unused imports, spacing etc.).
+* Avoid unnecessary abbreviations for variable names. Code is more often read
+  than written.
+* When writing a help text for a new command-line option, look at the output of
+  ``cutadapt --help`` and try to make it look nice and short.
+* In comments and documentation, capitalize FASTQ, BWA, CPU etc.
+

MANIFEST.in

+include CHANGES.rst
+include CITATION
+include LICENSE
+include README.rst
+include pyproject.toml
+include doc/*.rst
+include doc/conf.py
+include doc/Makefile
+include src/cutadapt/*.c
+include src/cutadapt/*.pyx
+include tests/*.py
+graft tests/data
+graft tests/cut

PKG-INFO

-Metadata-Version: 2.1
-Name: cutadapt
-Version: 2.5
-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: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master
-            :target: https://travis-ci.org/marcelm/cutadapt
-            :alt:
-        
-        .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master
-            :target: https://pypi.python.org/pypi/cutadapt
-            :alt:
-        
-        .. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg
-            :target: https://codecov.io/gh/marcelm/cutadapt
-            :alt:
-        
-        ========
-        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 :: 3
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.4
-Provides-Extra: dev

README.rst

@@ -10,6 +10,11 @@
     :target: https://codecov.io/gh/marcelm/cutadapt
     :alt:
 
+.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
+    :target: http://bioconda.github.io/recipes/cutadapt/README.html
+    :alt: install with bioconda
+
+
 ========
 Cutadapt
 ========
@@ -24,13 +29,16 @@ 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.
+sequences in an error-tolerant way. It can also modify and filter single-end
+and paired-end reads in various ways. Adapter sequences can contain IUPAC
+wildcard characters. Cutadapt can also demultiplex your reads.
+
+Cutadapt is available under the terms of the MIT license.
 
-Cutadapt comes with an extensive suite of automated tests and is available under
-the terms of the MIT license.
+Cutadapt development was started at `TU Dortmund University <https://www.tu-dortmund.de>`_
+in the group of `Prof. Dr. Sven Rahmann <https://www.rahmannlab.de/>`_.
+It is currently being developed within
+`NBIS (National Bioinformatics Infrastructure Sweden) <https://nbis.se/>`_.
 
 If you use Cutadapt, please cite
 `DOI:10.14806/ej.17.1.200 <http://dx.doi.org/10.14806/ej.17.1.200>`_ .
@@ -44,4 +52,4 @@ Links
 * `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>`_
+* `Wrapper for the Galaxy platform <https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt>`_

buildwheels.sh

+#!/bin/bash
+#
+# Build manylinux1 wheels for cutadapt. Based on the example at
+# <https://github.com/pypa/python-manylinux-demo>
+#
+# It is best to run this in a fresh clone of the repository!
+#
+# Run this within the repository root:
+#   docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/buildwheels.sh
+#
+# The wheels will be put into the wheelhouse/ subdirectory.
+#
+# For interactive tests:
+#   docker run -it -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /bin/bash
+
+set -xeuo pipefail
+
+MANYLINUX=quay.io/pypa/manylinux2010_x86_64
+
+# For convenience, if this script is called from outside of a docker container,
+# it starts a container and runs itself inside of it.
+if ! grep -q docker /proc/1/cgroup; then
+  # We are not inside a container
+  docker pull ${MANYLINUX}
+  exec docker run --rm -v $(pwd):/io ${MANYLINUX} /io/$0
+fi
+
+# Strip binaries (copied from multibuild)
+STRIP_FLAGS=${STRIP_FLAGS:-"-Wl,-strip-all"}
+export CFLAGS="${CFLAGS:-$STRIP_FLAGS}"
+export CXXFLAGS="${CXXFLAGS:-$STRIP_FLAGS}"
+
+# We require Python 3.5+
+rm /opt/python/cp27* /opt/python/cp34*
+
+PYBINS="/opt/python/*/bin"
+HAS_CYTHON=0
+for PYBIN in ${PYBINS}; do
+#    ${PYBIN}/pip install -r /io/requirements.txt
+    ${PYBIN}/pip wheel /io/ -w wheelhouse/
+done
+
+# Bundle external shared libraries into the wheels
+for whl in wheelhouse/cutadapt-*.whl; do
+    auditwheel repair "$whl" --plat manylinux1_x86_64 -w repaired/
+done
+
+# Created files are owned by root, so fix permissions.
+chown -R --reference=/io/setup.py repaired/
+mv repaired/*.whl /io/dist/
+
+# TODO Install packages and test them
+#for PYBIN in ${PYBINS}; do
+#    ${PYBIN}/pip install cutadapt --no-index -f /io/wheelhouse
+#    (cd $HOME; ${PYBIN}/nosetests ...)
+#done

debian/changelog

+python-cutadapt (2.6-1) unstable; urgency=medium
+
+  * Team upload
+  * New upstream version
+  * Now fetching sources from github
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 30 Oct 2019 10:17:14 +0100
+
 python-cutadapt (2.5-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 12),
                python3-setuptools-scm,
                python3-pytest-timeout,
                python3-xopen (>= 0.5.0),
-               python3-dnaio,
+               python3-dnaio (>= 0.4),
                cython3
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-cutadapt

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: python-cutadapt
-Source: http://pypi.python.org/pypi/cutadapt
+Source: https://github.com/marcelm/cutadapt
 
 Files: *
 Copyright: 2010-2015 Marcel Martin <marcel.martin@scilifelab.se>

debian/patches/skip_cutadapt_executable_test.patch

@@ -4,9 +4,11 @@ Description: Since built-time tests are running before installation,
  executables are not available yet.
 
 
---- a/tests/test_commandline.py
-+++ b/tests/test_commandline.py
-@@ -541,6 +541,7 @@
+Index: python-cutadapt/tests/test_commandline.py
+===================================================================
+--- python-cutadapt.orig/tests/test_commandline.py
++++ python-cutadapt/tests/test_commandline.py
+@@ -561,6 +561,7 @@ def test_negative_length(run):
      run('--length -5', 'shortened-negative.fastq', 'small.fastq')
  
  

debian/rules

@@ -34,3 +34,6 @@ endif
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf src/cutadapt.egg-info/ .pytest_cache
+	rm -f src/cutadapt/_version.py
+	# cython-generated files
+	rm -f src/cutadapt/_align.c src/cutadapt/qualtrim.c

debian/watch

 version=4
-opts=uversionmangle=s/(rc|a|b|c)/~$1/ \
-https://pypi.debian.net/cutadapt/cutadapt-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
\ No newline at end of file
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%cutadapt-$1.tar.gz%" \
+ https://github.com/marcelm/cutadapt/tags \
+ (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
+#uversionmangle=s/(rc|a|b|c)/~$1/

doc/_static/adapters.svg

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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
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+   xmlns:dc="http://purl.org/dc/elements/1.1/"
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doc/guide.rst

@@ -20,9 +20,8 @@ Compressed in- and output files are also supported::
 Cutadapt searches for the adapter in all reads and removes it when it finds it.
 Unless you use a filtering option, all reads that were present in the input file
 will also be present in the output file, some of them trimmed, some of them not.
-Even reads that were trimmed entirely (because the adapter was found in the very
-beginning) are output. All of this can be changed with command-line options,
-explained further down.
+Even reads that were trimmed to a length of zero are output. All of this can be
+changed with command-line options, explained further down.
 
 :ref:`Trimming of paired-end data <paired-end>` is also supported.
 
@@ -30,30 +29,18 @@ explained further down.
 Input and output file formats
 -----------------------------
 
-Input and output files need to be in FASTA or FASTQ format. Reading and writing
-compressed file formats ``.gz``, ``.bz2`` or ``.xz`` is also supported. Cutadapt
-uses ``pigz`` internally if possible to speed up writing and reading of
-gzipped files.
+The supported input and output file formats are FASTA and FASTQ, with
+optional compression.
 
 The input file format is recognized from the file name extension. If the
 extension was not recognized or when Cutadapt reads from standard input,
 the contents are inspected instead.
 
 The output file format is also recognized from the file name extension. If the
-extensions was not recognized or when Cutadapt writes to standard input, the
+extensions was not recognized or when Cutadapt writes to standard output, the
 same format as the input is used for the output.
 
-You can use this to convert from FASTQ to FASTA (without doing any adapter
-trimming)::
-
-    cutadapt -o output.fasta.gz input.fastq.gz
-
-When you want to do the same (read FASTQ, write FASTA), but want to write to
-standard output, you need to use ``--fasta`` instead because there is no
-output file name::
-
-    cutadapt --fasta input.fastq.gz > out.fasta
-
+See also :ref:`file format conversion <file-format-conversion>`.
 
 .. _compressed-files:
 
@@ -76,13 +63,15 @@ The default compression level for gzip output is 6. Use option ``-Z`` to
 change this to level 1. The files need more space, but it is faster and
 therefore a good choice for short-lived intermediate files.
 
+If available, Cutadapt uses `pigz <https://zlib.net/pigz/>`_ to speed up
+writing and reading of gzipped files.
+
 
 Standard input and output
 -------------------------
 
 If no output file is specified via the ``-o`` option, then the output is sent to
-the standard output stream. Instead of the example command line from above, you
-can therefore also write::
+the standard output stream. Example::
 
     cutadapt -a AACCGGTT input.fastq > output.fastq
 
@@ -142,17 +131,15 @@ the output will be done in a single thread and therefore be a bottleneck.
 
 There are some limitations at the moment:
 
-* Multi-core Cutadapt can only write to output files given by ``-o`` and ``-p``.
-  This implies that the following command-line arguments are not compatible with
+* The following command-line arguments are not compatible with
   multi-core:
 
       - ``--info-file``
       - ``--rest-file``
       - ``--wildcard-file``
+      - ``--format``
 
-* Multi-core is also not compatible with ``--format``
-
-* Multi-core is also not available when you use Cutadapt for demultiplexing.
+* Multi-core is not available when you use Cutadapt for demultiplexing.
 
 If you try to use multiple cores with an incompatible commandline option, you
 will get an error message.
@@ -171,7 +158,7 @@ Some of these limitations will be lifted in the future, as time allows.
 Speed-up tricks
 ---------------
 
-There are several tricks for limiting wall-clock time while using cutadapt.
+There are several tricks for limiting wall-clock time while using Cutadapt.
 
 ``-Z`` (alternatively ``--compression-level=1``) can be used to limit the
 amount of CPU time which is spent on the compression of output files.
@@ -1567,7 +1554,7 @@ to use ``{name1}}`` and ``{name2}`` in both output file name templates. For exam
         -e 0.15 --no-indels \
         -g file:barcodes_fwd.fasta \
         -G file:barcodes_rev.fasta \
-        -o trimmed-{name1}-{name2}.1.fastq.gz -p trimmed-{name1}-{name2}.2.fastq.gz \
+        -o {name1}-{name2}.1.fastq.gz -p {name1}-{name2}.2.fastq.gz \
         input.1.fastq.gz input.2.fastq.gz
 
 The ``{name1}`` will be replaced with the name of the best-matching R1 adapter and ``{name2}}`` will
@@ -1583,6 +1570,26 @@ Read the :ref:`demultiplexing <demultiplexing>` section for how to choose the er
 Also, the tips below about how to speed up demultiplexing apply even with combinatorial
 demultiplexing.
 
+When doing the above, you will end up with lots of files named ``first-second.x.fastq.gz``, where
+*first* is the name of the first indexed adapter and *second* is the name of the second indexed
+adapter, and *x* is 1 or 2. Each indexed adapter combination may correspond to a sample name and
+you may want to name your files according to the sample name, not the name of the adapters.
+Cutadapt does not have built-in functionality to achieve this, but you can use an external
+tool such as ``mmv`` (“multiple move”). First, create a list of patterns in ``patterns.txt``::
+
+    fwdindex1-revindex1.[12].fastq.gz sampleA.#1.fastq.gz
+    fwdindex1-revindex2.[12].fastq.gz sampleB.#1.fastq.gz
+    fwdindex1-revindex3.[12].fastq.gz sampleC.#1.fastq.gz
+    fwdindex2-revindex1.[12].fastq.gz sampleD.#1.fastq.gz
+    fwdindex2-revindex2.[12].fastq.gz sampleE.#1.fastq.gz
+    ...
+
+Here, *fwdindex1*/*revindex1* etc. are the names of indexes, and *sampleA* etc.
+are your sample names. Then rename all files at once with ::
+
+    mmv < patterns.txt
+
+
 .. versionadded:: 2.4