Skip to content

Commit 92e3f40

Browse files
authored
Release 1.5.2 (#529)
* Release javadoc * Release documentation site * Update CHANGELOG
1 parent c941838 commit 92e3f40

File tree

287 files changed

+1001
-951
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

287 files changed

+1001
-951
lines changed

CHANGELOG.md

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,9 @@ The meaning of each entry is user-based and can be found in our
88

99
## [Unreleased]
1010

11+
12+
## [1.5.2]
13+
1114
### Fixed
1215
- Allow special characters in advance java-property for barcode sequence/quality separators
1316

@@ -305,3 +308,4 @@ First pre-release
305308
[1.4.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.1
306309
[1.5.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.0
307310
[1.5.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.1
311+
[1.5.2]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.2

docs/_data/index.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
ReadTools:
2-
version: 1.5.1
3-
timestamp: 27-49-2018 03:49:16
2+
version: 1.5.2
3+
timestamp: 30-57-2018 12:57:55
44

55
tools:
66
- group: Diagnostics and Quality Control

docs/javadoc/allclasses-frame.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,9 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>All Classes (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>All Classes (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
99
<script type="text/javascript" src="script.js"></script>
1010
</head>

docs/javadoc/allclasses-noframe.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,9 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>All Classes (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>All Classes (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
99
<script type="text/javascript" src="script.js"></script>
1010
</head>

docs/javadoc/constant-values.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>Constant Field Values (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>Constant Field Values (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
99
<script type="text/javascript" src="script.js"></script>
1010
</head>
1111
<body>
1212
<script type="text/javascript"><!--
1313
try {
1414
if (location.href.indexOf('is-external=true') == -1) {
15-
parent.document.title="Constant Field Values (ReadTools 1.5.1 API)";
15+
parent.document.title="Constant Field Values (ReadTools 1.5.2 API)";
1616
}
1717
}
1818
catch(err) {

docs/javadoc/deprecated-list.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>Deprecated List (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>Deprecated List (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
99
<script type="text/javascript" src="script.js"></script>
1010
</head>
1111
<body>
1212
<script type="text/javascript"><!--
1313
try {
1414
if (location.href.indexOf('is-external=true') == -1) {
15-
parent.document.title="Deprecated List (ReadTools 1.5.1 API)";
15+
parent.document.title="Deprecated List (ReadTools 1.5.2 API)";
1616
}
1717
}
1818
catch(err) {

docs/javadoc/help-doc.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>API Help (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>API Help (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
99
<script type="text/javascript" src="script.js"></script>
1010
</head>
1111
<body>
1212
<script type="text/javascript"><!--
1313
try {
1414
if (location.href.indexOf('is-external=true') == -1) {
15-
parent.document.title="API Help (ReadTools 1.5.1 API)";
15+
parent.document.title="API Help (ReadTools 1.5.2 API)";
1616
}
1717
}
1818
catch(err) {

docs/javadoc/index-all.html

Lines changed: 14 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>Index (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>Index (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
99
<script type="text/javascript" src="script.js"></script>
1010
</head>
1111
<body>
1212
<script type="text/javascript"><!--
1313
try {
1414
if (location.href.indexOf('is-external=true') == -1) {
15-
parent.document.title="Index (ReadTools 1.5.1 API)";
15+
parent.document.title="Index (ReadTools 1.5.2 API)";
1616
}
1717
}
1818
catch(err) {
@@ -479,6 +479,14 @@ <h2 class="title">D</h2>
479479
<dd>
480480
<div class="block">Decodes a single-end Distmap String.</div>
481481
</dd>
482+
<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>
483+
<dd>
484+
<div class="block">Default regular expression to split barcodes.</div>
485+
</dd>
486+
<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>
487+
<dd>
488+
<div class="block">Default regular expression to split barcode qualities.</div>
489+
</dd>
482490
<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>
483491
<dd>
484492
<div class="block">Output extension for metric files.</div>
@@ -667,7 +675,7 @@ <h2 class="title">E</h2>
667675
<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>
668676
<dd>
669677
<div class="block">Extract and remove the barcode from the read name, splitting the barcodes in the read name
670-
using <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>.</div>
678+
using <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>.</div>
671679
</dd>
672680
</dl>
673681
<a name="I:F">
@@ -930,7 +938,7 @@ <h2 class="title">G</h2>
930938
<dd>&nbsp;</dd>
931939
<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>
932940
<dd>
933-
<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>
941+
<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>
934942
</dd>
935943
<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>
936944
<dd>

docs/javadoc/index.html

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
6-
<title>ReadTools 1.5.1 API</title>
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
6+
<title>ReadTools 1.5.2 API</title>
77
<script type="text/javascript">
88
tmpTargetPage = "" + window.location.search;
99
if (tmpTargetPage != "" && tmpTargetPage != "undefined")

docs/javadoc/org/magicdgs/readtools/Main.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
<!-- NewPage -->
33
<html lang="en">
44
<head>
5-
<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
6-
<title>Main (ReadTools 1.5.1 API)</title>
7-
<meta name="date" content="2018-08-27">
5+
<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
6+
<title>Main (ReadTools 1.5.2 API)</title>
7+
<meta name="date" content="2018-08-30">
88
<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
99
<script type="text/javascript" src="../../../script.js"></script>
1010
</head>
1111
<body>
1212
<script type="text/javascript"><!--
1313
try {
1414
if (location.href.indexOf('is-external=true') == -1) {
15-
parent.document.title="Main (ReadTools 1.5.1 API)";
15+
parent.document.title="Main (ReadTools 1.5.2 API)";
1616
}
1717
}
1818
catch(err) {

0 commit comments

Comments
 (0)