Loading CHANGES.rst +100 −0 Original line number Diff line number Diff line Loading @@ -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) ------------------ Loading LICENSE +1 −1 Original line number Diff line number Diff line 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 Loading MANIFEST.indeleted 100644 → 0 +0 −13 Original line number Diff line number Diff line 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 +6 −6 Original line number Diff line number Diff line 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 Loading @@ -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 Loading @@ -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>`_ . Loading @@ -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 +2 −2 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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>`_ . Loading Loading
CHANGES.rst +100 −0 Original line number Diff line number Diff line Loading @@ -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) ------------------ Loading
LICENSE +1 −1 Original line number Diff line number Diff line 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 Loading
MANIFEST.indeleted 100644 → 0 +0 −13 Original line number Diff line number Diff line 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 +6 −6 Original line number Diff line number Diff line 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 Loading @@ -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 Loading @@ -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>`_ . Loading @@ -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 +2 −2 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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>`_ . Loading
