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Release 1.0.0 (#235)
Release version 1.0.0, including some functionality regarding the releasing process: * Use gitVerstion tag for a more verbose way of distinguish developmental versions * Add a release script to generate the tag and generate the javadoc * Update the current javadoc and doc pages version (required for correct display) * Update README to clarify that the SemVer refers to user-functionality
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‎CHANGELOG.md‎

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# Change Log
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All notable changes to this project will be documented in this file.
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## [Unreleased] - 1.0.0
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## 1.0.0 - 2017-05-18
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### Fixed
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- MD5 file digest for FASTQ is for the file itself and not its content.
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[Unreleased]: https://github.com/magicDGS/ReadTools/tree/master
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[1.0.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.0.0
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[0.3.0]: https://github.com/magicDGS/ReadTools/releases/tag/0.3.0
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[0.2.3]: https://github.com/magicDGS/ReadTools/releases/tag/0.2.2
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[0.2.2]: https://github.com/magicDGS/ReadTools/releases/tag/0.2.2

‎README.md‎

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## Versioning and changelog
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We use [Semantic Versioning (SemVer)](http://semver.org/) (_MAJOR.MINOR.PATCH_). The [CHANGELOG] will be updated accordingly after Pull Requests to follow the convention:
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We use [Semantic Versioning (SemVer)](http://semver.org/) (_MAJOR.MINOR.PATCH_) for the user-side, but not the API. The [CHANGELOG] will be updated accordingly after Pull Requests to follow the convention:
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1. Backwards-compatible bug fixes: Add a __Fixed__ entry.
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These fixes will be released after they are included, by bumping the _PATCH_ number.
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3. Backwards-incompatible changes: Add a __Changed__ entry.
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These changes will be included after a month from the last release, by bumping the _MAJOR_ number and reset _MINOR_ and _PATCH_ to 0.
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Changes are distinguished by the ones corresponding to API changes alone or if it have some effect on the user side.
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Our API for developers is still not stable, and changes for developers are reflected in under a __API change__ entry from version 1.0.0 onwards.
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‎build.gradle‎

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}
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}
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// it is a release only if the boolean is a release and the git version does not contain .dirty
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final isRelease = !gitVersion().contains(".dirty") && Boolean.getBoolean("release")
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group = 'org.magicdgs'
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version = hashedVersion('1.0.0')
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version = (isRelease ? gitVersion() : gitVersion() + "-SNAPSHOT").replaceAll(".dirty", "")
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description = """Tools for sequencing barcoded read data (in FASTQ/BAM format)"""
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def developer = "Daniel Gomez-Sanchez"
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mainClassName = group + "." + rootProject.name.toLowerCase() + ".Main"
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// method for defining the version using the build-number from git-hash
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// TODO: this should be removed for https://github.com/magicDGS/ReadTools/issues/184
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def hashedVersion(String semVer) {
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def hashedVersion = semVer + "-" + versionDetails().gitHash
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return (gitVersion().contains("dirty")) ? hashedVersion + "-SNAPSHOT" : hashedVersion
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}
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repositories {
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mavenCentral()
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maven {

‎docs/_data/sidebars/home_sidebar.yml‎

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entries:
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- title: Sidebar
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product: ReadTools
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version: 1.0.0-SNAPSHOT
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version: 1.0.0
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folders:
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- title: ReadTools

‎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 May 17 12:40:11 CEST 2017 -->
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<title>All Classes (ReadTools 1.0.0-06e6f8ac28 API)</title>
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 14:00:27 CEST 2017 -->
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<title>All Classes (ReadTools 1.0.0 API)</title>
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<meta name="date" content="2017-05-17">
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<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
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<script type="text/javascript" src="script.js"></script>

‎docs/javadoc/allclasses-noframe.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 May 17 12:40:11 CEST 2017 -->
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<title>All Classes (ReadTools 1.0.0-06e6f8ac28 API)</title>
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 14:00:27 CEST 2017 -->
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<title>All Classes (ReadTools 1.0.0 API)</title>
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‎docs/javadoc/constant-values.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 May 17 12:40:11 CEST 2017 -->
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<title>Constant Field Values (ReadTools 1.0.0-06e6f8ac28 API)</title>
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 14:00:27 CEST 2017 -->
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<title>Constant Field Values (ReadTools 1.0.0 API)</title>
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<script type="text/javascript"><!--
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try {
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if (location.href.indexOf('is-external=true') == -1) {
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parent.document.title="Constant Field Values (ReadTools 1.0.0-06e6f8ac28 API)";
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parent.document.title="Constant Field Values (ReadTools 1.0.0 API)";
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‎docs/javadoc/deprecated-list.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 May 17 12:40:11 CEST 2017 -->
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<title>Deprecated List (ReadTools 1.0.0-06e6f8ac28 API)</title>
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 14:00:27 CEST 2017 -->
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<title>Deprecated List (ReadTools 1.0.0 API)</title>
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<script type="text/javascript"><!--
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parent.document.title="Deprecated List (ReadTools 1.0.0-06e6f8ac28 API)";
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parent.document.title="Deprecated List (ReadTools 1.0.0 API)";
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‎docs/javadoc/help-doc.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 May 17 12:40:11 CEST 2017 -->
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<title>API Help (ReadTools 1.0.0-06e6f8ac28 API)</title>
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 14:00:27 CEST 2017 -->
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<title>API Help (ReadTools 1.0.0 API)</title>
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parent.document.title="API Help (ReadTools 1.0.0 API)";
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‎docs/javadoc/index-all.html‎

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<!-- NewPage -->
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<html lang="en">
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 12:40:11 CEST 2017 -->
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<title>Index (ReadTools 1.0.0-06e6f8ac28 API)</title>
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<!-- Generated by javadoc (1.8.0_60) on Wed May 17 14:00:27 CEST 2017 -->
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<title>Index (ReadTools 1.0.0 API)</title>
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parent.document.title="Index (ReadTools 1.0.0-06e6f8ac28 API)";
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parent.document.title="Index (ReadTools 1.0.0 API)";
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