066be082ec
v3.5 (2021-09-29) ----------------- * :issue:`555`: Add support for dumping statistics in JSON format using ``--json``. * :issue:`541`: Add a "Read fate breakdown" section heading to the report, and also add statistics for reads discarded because of ``--discard-untrimmed`` and ``--discard-trimmed``. With this, the numbers in that section should add up to 100%. * Add option ``-Q``, which allows to specify a quality-trimming threshold for R2 that is different from the one for R1. * :issue:`567`: Add ``noindels`` adapter-trimming parameter. You can now write ``-a "ADAPTER;noindels"`` to disallow indels for a single adapter only. * :issue:`570`: Fix ``--pair-adapters`` not finding some pairs when reads contain more than one adapter. * :issue:`524`: Fix a memory leak when using ``--info-file`` with multiple cores. * :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.
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58 lines
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@comment $NetBSD: PLIST,v 1.3 2022/01/17 09:03:10 adam Exp $
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bin/cutadapt-${PYVERSSUFFIX}
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${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
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${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
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${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
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${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
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${PYSITELIB}/${EGG_INFODIR}/requires.txt
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${PYSITELIB}/${EGG_INFODIR}/top_level.txt
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${PYSITELIB}/cutadapt/__init__.py
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${PYSITELIB}/cutadapt/__init__.pyc
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${PYSITELIB}/cutadapt/__init__.pyo
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${PYSITELIB}/cutadapt/__main__.py
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${PYSITELIB}/cutadapt/__main__.pyc
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${PYSITELIB}/cutadapt/__main__.pyo
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${PYSITELIB}/cutadapt/_align.so
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${PYSITELIB}/cutadapt/_version.py
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${PYSITELIB}/cutadapt/_version.pyc
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${PYSITELIB}/cutadapt/_version.pyo
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${PYSITELIB}/cutadapt/adapters.py
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${PYSITELIB}/cutadapt/adapters.pyc
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${PYSITELIB}/cutadapt/adapters.pyo
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${PYSITELIB}/cutadapt/align.py
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${PYSITELIB}/cutadapt/align.pyc
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${PYSITELIB}/cutadapt/align.pyo
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${PYSITELIB}/cutadapt/filters.py
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${PYSITELIB}/cutadapt/filters.pyc
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${PYSITELIB}/cutadapt/filters.pyo
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${PYSITELIB}/cutadapt/json.py
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${PYSITELIB}/cutadapt/json.pyc
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${PYSITELIB}/cutadapt/json.pyo
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${PYSITELIB}/cutadapt/log.py
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${PYSITELIB}/cutadapt/log.pyc
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${PYSITELIB}/cutadapt/log.pyo
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${PYSITELIB}/cutadapt/modifiers.py
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${PYSITELIB}/cutadapt/modifiers.pyc
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${PYSITELIB}/cutadapt/modifiers.pyo
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${PYSITELIB}/cutadapt/parser.py
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${PYSITELIB}/cutadapt/parser.pyc
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${PYSITELIB}/cutadapt/parser.pyo
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${PYSITELIB}/cutadapt/pipeline.py
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${PYSITELIB}/cutadapt/pipeline.pyc
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${PYSITELIB}/cutadapt/pipeline.pyo
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${PYSITELIB}/cutadapt/qualtrim.so
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${PYSITELIB}/cutadapt/report.py
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${PYSITELIB}/cutadapt/report.pyc
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${PYSITELIB}/cutadapt/report.pyo
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${PYSITELIB}/cutadapt/statistics.py
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${PYSITELIB}/cutadapt/statistics.pyc
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${PYSITELIB}/cutadapt/statistics.pyo
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${PYSITELIB}/cutadapt/steps.py
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${PYSITELIB}/cutadapt/steps.pyc
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${PYSITELIB}/cutadapt/steps.pyo
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${PYSITELIB}/cutadapt/tokenizer.py
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${PYSITELIB}/cutadapt/tokenizer.pyc
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${PYSITELIB}/cutadapt/tokenizer.pyo
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${PYSITELIB}/cutadapt/utils.py
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${PYSITELIB}/cutadapt/utils.pyc
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${PYSITELIB}/cutadapt/utils.pyo
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