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Release 1.2.0 (#392)
* Release javadoc * Release documentation site * Update CHANGELOG
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‎CHANGELOG.md‎

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## [Unreleased]
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## [1.2.0]
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### Fixed
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- User error error for corrupted BAM file instead of unexpected error
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[0.2.3]: https://github.com/magicDGS/ReadTools/releases/tag/0.2.2
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[0.3.0]: https://github.com/magicDGS/ReadTools/releases/tag/0.3.0
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[1.0.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.0.0
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[1.1.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.1.0
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[1.1.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.1.0
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[1.2.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.2.0

‎docs/_data/index.yml‎

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ReadTools:
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version: 1.1.0
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timestamp: 04-49-2017 12:49:37
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version: 1.2.0
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timestamp: 29-03-2018 04:03:32
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tools:
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- group: Diagnostics and Quality Control Tools
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summary: Tools for Diagnostics and Quality Control
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- group: Diagnostics and Quality Control
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summary: Tools that collect sequencing quality-related and comparative metrics
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components:
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- name: QualityEncodingDetector
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summary: Detects the quality encoding format for all kind of sources for ReadTools.
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utilities:
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- group: Read Filters
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summary: Read Filters used by the engine to select reads to be included for analysis
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summary: Applied by engine to select reads for analysis
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components:
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- name: AlignmentAgreesWithHeaderReadFilter
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summary: Filters out reads where the alignment does not match the contents of the header

‎docs/javadoc/allclasses-frame.html‎

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<!-- NewPage -->
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<html lang="en">
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<head>
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<!-- Generated by javadoc (1.8.0_60) on Wed Oct 04 12:49:35 CEST 2017 -->
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<title>All Classes (ReadTools 1.1.0 API)</title>
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<meta name="date" content="2017-10-04">
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<!-- Generated by javadoc (1.8.0_60) on Mon Jan 29 16:03:30 CET 2018 -->
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<title>All Classes (ReadTools 1.2.0 API)</title>
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<meta name="date" content="2018-01-29">
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</head>
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<li><a href="org/magicdgs/readtools/utils/read/writer/SplitGATKWriter.html" title="class in org.magicdgs.readtools.utils.read.writer" target="classFrame">SplitGATKWriter</a></li>
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<li><a href="org/magicdgs/readtools/tools/conversion/StandardizeReads.html" title="class in org.magicdgs.readtools.tools.conversion" target="classFrame">StandardizeReads</a></li>
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<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/TrailingNtrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">TrailingNtrimmer</a></li>
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<li><a href="org/magicdgs/readtools/tools/trimming/TrimAndFilterPipeline.html" title="class in org.magicdgs.readtools.tools.trimming" target="classFrame">TrimAndFilterPipeline</a></li>
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<li><a href="org/magicdgs/readtools/utils/trimming/TrimAndFilterPipeline.html" title="class in org.magicdgs.readtools.utils.trimming" target="classFrame">TrimAndFilterPipeline</a></li>
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<li><a href="org/magicdgs/readtools/cmd/argumentcollections/TrimmerPluginArgumentCollection.html" title="class in org.magicdgs.readtools.cmd.argumentcollections" target="classFrame">TrimmerPluginArgumentCollection</a></li>
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<li><a href="org/magicdgs/readtools/cmd/plugin/TrimmerPluginDescriptor.html" title="class in org.magicdgs.readtools.cmd.plugin" target="classFrame">TrimmerPluginDescriptor</a></li>
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<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/TrimmingFunction.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">TrimmingFunction</a></li>
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<li><a href="org/magicdgs/readtools/utils/trimming/TrimmingUtil.html" title="class in org.magicdgs.readtools.utils.trimming" target="classFrame">TrimmingUtil</a></li>
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<li><a href="org/magicdgs/readtools/tools/trimming/TrimReads.html" title="class in org.magicdgs.readtools.tools.trimming" target="classFrame">TrimReads</a></li>
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<li><a href="org/magicdgs/readtools/tools/trimming/TrimReadsTrimmerPluginArgumentCollection.html" title="class in org.magicdgs.readtools.tools.trimming" target="classFrame">TrimReadsTrimmerPluginArgumentCollection</a></li>
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‎docs/javadoc/allclasses-noframe.html‎

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<!-- Generated by javadoc (1.8.0_60) on Mon Jan 29 16:03:30 CET 2018 -->
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<title>All Classes (ReadTools 1.2.0 API)</title>
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<meta name="date" content="2018-01-29">
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<li><a href="org/magicdgs/readtools/tools/conversion/StandardizeReads.html" title="class in org.magicdgs.readtools.tools.conversion">StandardizeReads</a></li>
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<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/TrailingNtrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming">TrailingNtrimmer</a></li>
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<li><a href="org/magicdgs/readtools/tools/trimming/TrimAndFilterPipeline.html" title="class in org.magicdgs.readtools.tools.trimming">TrimAndFilterPipeline</a></li>
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<li><a href="org/magicdgs/readtools/utils/trimming/TrimAndFilterPipeline.html" title="class in org.magicdgs.readtools.utils.trimming">TrimAndFilterPipeline</a></li>
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<li><a href="org/magicdgs/readtools/metrics/TrimmerMetric.html" title="class in org.magicdgs.readtools.metrics">TrimmerMetric</a></li>
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<li><a href="org/magicdgs/readtools/cmd/argumentcollections/TrimmerPluginArgumentCollection.html" title="class in org.magicdgs.readtools.cmd.argumentcollections">TrimmerPluginArgumentCollection</a></li>
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<li><a href="org/magicdgs/readtools/utils/trimming/TrimmingUtil.html" title="class in org.magicdgs.readtools.utils.trimming">TrimmingUtil</a></li>
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<li><a href="org/magicdgs/readtools/tools/trimming/TrimReadsTrimmerPluginArgumentCollection.html" title="class in org.magicdgs.readtools.tools.trimming">TrimReadsTrimmerPluginArgumentCollection</a></li>
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