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Merged
magicDGS merged 3 commits into from
Aug 30, 2018
Merged

Release 1.5.2 #529

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5c810ea
Release javadoc
magicDGS Aug 30, 2018
8adf4a0
Release documentation site
magicDGS Aug 30, 2018
db11b9b
Update CHANGELOG
magicDGS Aug 30, 2018
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,9 @@ The meaning of each entry is user-based and can be found in our

## [Unreleased]


## [1.5.2]

### Fixed
- Allow special characters in advance java-property for barcode sequence/quality separators

Expand Down Expand Up @@ -305,3 +308,4 @@ First pre-release
[1.4.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.1
[1.5.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.0
[1.5.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.1
[1.5.2]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.2
4 changes: 2 additions & 2 deletions docs/_data/index.yml
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@@ -1,6 +1,6 @@
ReadTools:
version: 1.5.1
timestamp: 27-49-2018 03:49:16
version: 1.5.2
timestamp: 30-57-2018 12:57:55

tools:
- group: Diagnostics and Quality Control
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6 changes: 3 additions & 3 deletions docs/javadoc/allclasses-frame.html
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<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>All Classes (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>All Classes (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<script type="text/javascript" src="script.js"></script>
</head>
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<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>All Classes (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>All Classes (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<script type="text/javascript" src="script.js"></script>
</head>
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8 changes: 4 additions & 4 deletions docs/javadoc/constant-values.html
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<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>Constant Field Values (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>Constant Field Values (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
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<script type="text/javascript" src="script.js"></script>
</head>
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<script type="text/javascript"><!--
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if (location.href.indexOf('is-external=true') == -1) {
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<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>Deprecated List (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>Deprecated List (ReadTools 1.5.2 API)</title>
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<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>API Help (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>API Help (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<script type="text/javascript" src="script.js"></script>
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if (location.href.indexOf('is-external=true') == -1) {
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<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>Index (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>Index (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<script type="text/javascript" src="script.js"></script>
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Expand Down Expand Up @@ -479,6 +479,14 @@ <h2 class="title">D</h2>
<dd>
<div class="block">Decodes a single-end Distmap String.</div>
</dd>
<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT">DEFAULT_BARCODE_INDEX_SPLIT</a></span> - Static variable in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
<dd>
<div class="block">Default regular expression to split barcodes.</div>
</dd>
<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_QUALITY_SPLIT">DEFAULT_BARCODE_QUALITY_SPLIT</a></span> - Static variable in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
<dd>
<div class="block">Default regular expression to split barcode qualities.</div>
</dd>
<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html#DEFAULT_METRICS_EXTENSION">DEFAULT_METRICS_EXTENSION</a></span> - Static variable in interface org.magicdgs.readtools.utils.read.writer.<a href="org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html" title="interface in org.magicdgs.readtools.utils.read.writer">ReadToolsIOFormat</a></dt>
<dd>
<div class="block">Output extension for metric files.</div>
Expand Down Expand Up @@ -667,7 +675,7 @@ <h2 class="title">E</h2>
<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#extractBarcodesFromReadName-org.broadinstitute.hellbender.utils.read.GATKRead-">extractBarcodesFromReadName(GATKRead)</a></span> - Static method in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
<dd>
<div class="block">Extract and remove the barcode from the read name, splitting the barcodes in the read name
using <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>.</div>
using <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>.</div>
</dd>
</dl>
<a name="I:F">
Expand Down Expand Up @@ -930,7 +938,7 @@ <h2 class="title">G</h2>
<dd>&nbsp;</dd>
<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html#getBarcodes-java.lang.String-">getBarcodes(String)</a></span> - Method in enum org.magicdgs.readtools.utils.fastq.<a href="org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html" title="enum in org.magicdgs.readtools.utils.fastq">FastqReadNameEncoding</a></dt>
<dd>
<div class="block">Returns the barcodes in the read name (splitted by <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>).</div>
<div class="block">Returns the barcodes in the read name (splitted by <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>).</div>
</dd>
<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#getBarcodesAndQualitiesFromTags-org.broadinstitute.hellbender.utils.read.GATKRead-java.util.List-java.util.List-">getBarcodesAndQualitiesFromTags(GATKRead, List&lt;String&gt;, List&lt;String&gt;)</a></span> - Static method in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
<dd>
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<head>
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
<title>ReadTools 1.5.1 API</title>
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
<title>ReadTools 1.5.2 API</title>
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<title>Main (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
<title>Main (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
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<script type="text/javascript" src="../../../script.js"></script>
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if (location.href.indexOf('is-external=true') == -1) {
parent.document.title="Main (ReadTools 1.5.1 API)";
parent.document.title="Main (ReadTools 1.5.2 API)";
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<title>RTDefaults (ReadTools 1.5.1 API)</title>
<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
<title>RTDefaults (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
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<script type="text/javascript" src="../../../script.js"></script>
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if (location.href.indexOf('is-external=true') == -1) {
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<meta name="date" content="2018-08-27">
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
<title>RTHelpConstants (ReadTools 1.5.2 API)</title>
<meta name="date" content="2018-08-30">
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<script type="text/javascript" src="../../../script.js"></script>
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if (location.href.indexOf('is-external=true') == -1) {
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<title>RTDeprecatedToolsRegistry (ReadTools 1.5.2 API)</title>
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<title>RTStandardArguments (ReadTools 1.5.2 API)</title>
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<meta name="date" content="2018-08-30">
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