Skip to content

Commit 1eca4d2

Browse files
authored
Release 1.5.1 (#523)
* Release javadoc * Release documentation site * Update CHANGELOG
1 parent a5eab2d commit 1eca4d2

287 files changed

Lines changed: 1302 additions & 1087 deletions

File tree

Some content is hidden

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

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+
## [1.5.1]
13+
1114
### Fixed
1215
- Add message for unknown command referring to a legacy pre-release tool
1316
- Documentation update of SRA Hadbook link (previous is currently unavailable)
@@ -296,3 +299,4 @@ First pre-release
296299
[1.4.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.0
297300
[1.4.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.1
298301
[1.5.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.0
302+
[1.5.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.1

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: 1.5.0
3-
timestamp: 27-06-2018 06:06:39
2+
version: 1.5.1
3+
timestamp: 27-49-2018 03:49:16
44

55
tools:
66
- group: Diagnostics and Quality Control

docs/javadoc/allclasses-frame.html

Lines changed: 6 additions & 5 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 Fri Jul 27 18:06:33 GMT 2018 -->
6-
<title>All Classes (ReadTools 1.5.0 API)</title>
7-
<meta name="date" content="2018-07-27">
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">
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
<h1 class="bar">All&nbsp;Classes</h1>
1313
<div class="indexContainer">
1414
<ul>
15-
<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/ApplyTrimResultReadTransfomer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">ApplyTrimResultReadTransfomer</a></li>
15+
<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/ApplyTrimResultReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">ApplyTrimResultReadTransformer</a></li>
1616
<li><a href="org/magicdgs/readtools/tools/barcodes/AssignReadGroupByBarcode.html" title="class in org.magicdgs.readtools.tools.barcodes" target="classFrame">AssignReadGroupByBarcode</a></li>
1717
<li><a href="org/magicdgs/readtools/tools/barcodes/dictionary/decoder/BarcodeDecoder.html" title="class in org.magicdgs.readtools.tools.barcodes.dictionary.decoder" target="classFrame">BarcodeDecoder</a></li>
1818
<li><a href="org/magicdgs/readtools/metrics/barcodes/BarcodeDetector.html" title="class in org.magicdgs.readtools.metrics.barcodes" target="classFrame">BarcodeDetector</a></li>
@@ -82,7 +82,8 @@ <h1 class="bar">All&nbsp;Classes</h1>
8282
<li><a href="org/magicdgs/readtools/cmd/programgroups/RTConversionProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups" target="classFrame">RTConversionProgramGroup</a></li>
8383
<li><a href="org/magicdgs/readtools/engine/RTDataSource.html" title="class in org.magicdgs.readtools.engine" target="classFrame">RTDataSource</a></li>
8484
<li><a href="org/magicdgs/readtools/RTDefaults.html" title="class in org.magicdgs.readtools" target="classFrame">RTDefaults</a></li>
85-
<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html" title="class in org.magicdgs.readtools.utils.fastq" target="classFrame">RTFastqContstants</a></li>
85+
<li><a href="org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html" title="class in org.magicdgs.readtools.cmd" target="classFrame">RTDeprecatedToolsRegistry</a></li>
86+
<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html" title="class in org.magicdgs.readtools.utils.fastq" target="classFrame">RTFastqConstants</a></li>
8687
<li><a href="org/magicdgs/readtools/documentation/RTGSONWorkUnit.html" title="class in org.magicdgs.readtools.documentation" target="classFrame">RTGSONWorkUnit</a></li>
8788
<li><a href="org/magicdgs/readtools/RTHelpConstants.html" title="class in org.magicdgs.readtools" target="classFrame">RTHelpConstants</a></li>
8889
<li><a href="org/magicdgs/readtools/documentation/RTHelpDoclet.html" title="class in org.magicdgs.readtools.documentation" target="classFrame">RTHelpDoclet</a></li>

docs/javadoc/allclasses-noframe.html

Lines changed: 6 additions & 5 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 Fri Jul 27 18:06:33 GMT 2018 -->
6-
<title>All Classes (ReadTools 1.5.0 API)</title>
7-
<meta name="date" content="2018-07-27">
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">
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
<h1 class="bar">All&nbsp;Classes</h1>
1313
<div class="indexContainer">
1414
<ul>
15-
<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/ApplyTrimResultReadTransfomer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming">ApplyTrimResultReadTransfomer</a></li>
15+
<li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/ApplyTrimResultReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming">ApplyTrimResultReadTransformer</a></li>
1616
<li><a href="org/magicdgs/readtools/tools/barcodes/AssignReadGroupByBarcode.html" title="class in org.magicdgs.readtools.tools.barcodes">AssignReadGroupByBarcode</a></li>
1717
<li><a href="org/magicdgs/readtools/tools/barcodes/dictionary/decoder/BarcodeDecoder.html" title="class in org.magicdgs.readtools.tools.barcodes.dictionary.decoder">BarcodeDecoder</a></li>
1818
<li><a href="org/magicdgs/readtools/metrics/barcodes/BarcodeDetector.html" title="class in org.magicdgs.readtools.metrics.barcodes">BarcodeDetector</a></li>
@@ -82,7 +82,8 @@ <h1 class="bar">All&nbsp;Classes</h1>
8282
<li><a href="org/magicdgs/readtools/cmd/programgroups/RTConversionProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups">RTConversionProgramGroup</a></li>
8383
<li><a href="org/magicdgs/readtools/engine/RTDataSource.html" title="class in org.magicdgs.readtools.engine">RTDataSource</a></li>
8484
<li><a href="org/magicdgs/readtools/RTDefaults.html" title="class in org.magicdgs.readtools">RTDefaults</a></li>
85-
<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html" title="class in org.magicdgs.readtools.utils.fastq">RTFastqContstants</a></li>
85+
<li><a href="org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html" title="class in org.magicdgs.readtools.cmd">RTDeprecatedToolsRegistry</a></li>
86+
<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html" title="class in org.magicdgs.readtools.utils.fastq">RTFastqConstants</a></li>
8687
<li><a href="org/magicdgs/readtools/documentation/RTGSONWorkUnit.html" title="class in org.magicdgs.readtools.documentation">RTGSONWorkUnit</a></li>
8788
<li><a href="org/magicdgs/readtools/RTHelpConstants.html" title="class in org.magicdgs.readtools">RTHelpConstants</a></li>
8889
<li><a href="org/magicdgs/readtools/documentation/RTHelpDoclet.html" title="class in org.magicdgs.readtools.documentation">RTHelpDoclet</a></li>

docs/javadoc/constant-values.html

Lines changed: 7 additions & 7 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 Fri Jul 27 18:06:33 GMT 2018 -->
6-
<title>Constant Field Values (ReadTools 1.5.0 API)</title>
7-
<meta name="date" content="2018-07-27">
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">
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 1.5.0 API)";
15+
parent.document.title="Constant Field Values (ReadTools 1.5.1 API)";
1616
}
1717
}
1818
catch(err) {
@@ -965,18 +965,18 @@ <h2 title="org.magicdgs">org.magicdgs.*</h2>
965965
<ul class="blockList">
966966
<li class="blockList">
967967
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
968-
<caption><span>org.magicdgs.readtools.utils.fastq.<a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html" title="class in org.magicdgs.readtools.utils.fastq">RTFastqContstants</a></span><span class="tabEnd">&nbsp;</span></caption>
968+
<caption><span>org.magicdgs.readtools.utils.fastq.<a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html" title="class in org.magicdgs.readtools.utils.fastq">RTFastqConstants</a></span><span class="tabEnd">&nbsp;</span></caption>
969969
<tr>
970970
<th class="colFirst" scope="col">Modifier and Type</th>
971971
<th scope="col">Constant Field</th>
972972
<th class="colLast" scope="col">Value</th>
973973
</tr>
974974
<tbody>
975975
<tr class="altColor">
976-
<td class="colFirst"><a name="org.magicdgs.readtools.utils.fastq.RTFastqContstants.ILLUMINA_NAME_BARCODE_DELIMITER">
976+
<td class="colFirst"><a name="org.magicdgs.readtools.utils.fastq.RTFastqConstants.ILLUMINA_NAME_BARCODE_DELIMITER">
977977
<!-- -->
978978
</a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
979-
<td><code><a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html#ILLUMINA_NAME_BARCODE_DELIMITER">ILLUMINA_NAME_BARCODE_DELIMITER</a></code></td>
979+
<td><code><a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html#ILLUMINA_NAME_BARCODE_DELIMITER">ILLUMINA_NAME_BARCODE_DELIMITER</a></code></td>
980980
<td class="colLast"><code>"#"</code></td>
981981
</tr>
982982
</tbody>

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 Fri Jul 27 18:06:33 GMT 2018 -->
6-
<title>Deprecated List (ReadTools 1.5.0 API)</title>
7-
<meta name="date" content="2018-07-27">
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">
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 1.5.0 API)";
15+
parent.document.title="Deprecated List (ReadTools 1.5.1 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 Fri Jul 27 18:06:33 GMT 2018 -->
6-
<title>API Help (ReadTools 1.5.0 API)</title>
7-
<meta name="date" content="2018-07-27">
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">
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 1.5.0 API)";
15+
parent.document.title="API Help (ReadTools 1.5.1 API)";
1616
}
1717
}
1818
catch(err) {

0 commit comments

Comments
 (0)