magicDGS · magicDGS · Aug 27, 2018 · Aug 27, 2018 · Aug 27, 2018 · Aug 27, 2018
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,9 @@ The meaning of each entry is user-based and can be found in our
 
 ## [Unreleased]
 
+
+## [1.5.1]
+
 ### Fixed
 - Add message for unknown command referring to a legacy pre-release tool
 - Documentation update of SRA Hadbook link (previous is currently unavailable)
@@ -296,3 +299,4 @@ First pre-release
 [1.4.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.0
 [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
diff --git a/docs/_data/index.yml b/docs/_data/index.yml
@@ -1,6 +1,6 @@
 ReadTools:
-  version: 1.5.0
-  timestamp: 27-06-2018 06:06:39
+  version: 1.5.1
+  timestamp: 27-49-2018 03:49:16
 
 tools:
   - group: Diagnostics and Quality Control

diff --git a/docs/javadoc/allclasses-frame.html b/docs/javadoc/allclasses-frame.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Fri Jul 27 18:06:33 GMT 2018 -->
-<title>All Classes (ReadTools 1.5.0 API)</title>
-<meta name="date" content="2018-07-27">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
 <body>
 <h1 class="bar">All&nbsp;Classes</h1>
 <div class="indexContainer">
 <ul>
-<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>
+<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>
 <li><a href="org/magicdgs/readtools/tools/barcodes/AssignReadGroupByBarcode.html" title="class in org.magicdgs.readtools.tools.barcodes" target="classFrame">AssignReadGroupByBarcode</a></li>
 <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>
 <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>
 <li><a href="org/magicdgs/readtools/cmd/programgroups/RTConversionProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups" target="classFrame">RTConversionProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/engine/RTDataSource.html" title="class in org.magicdgs.readtools.engine" target="classFrame">RTDataSource</a></li>
 <li><a href="org/magicdgs/readtools/RTDefaults.html" title="class in org.magicdgs.readtools" target="classFrame">RTDefaults</a></li>
-<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html" title="class in org.magicdgs.readtools.utils.fastq" target="classFrame">RTFastqContstants</a></li>
+<li><a href="org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html" title="class in org.magicdgs.readtools.cmd" target="classFrame">RTDeprecatedToolsRegistry</a></li>
+<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html" title="class in org.magicdgs.readtools.utils.fastq" target="classFrame">RTFastqConstants</a></li>
 <li><a href="org/magicdgs/readtools/documentation/RTGSONWorkUnit.html" title="class in org.magicdgs.readtools.documentation" target="classFrame">RTGSONWorkUnit</a></li>
 <li><a href="org/magicdgs/readtools/RTHelpConstants.html" title="class in org.magicdgs.readtools" target="classFrame">RTHelpConstants</a></li>
 <li><a href="org/magicdgs/readtools/documentation/RTHelpDoclet.html" title="class in org.magicdgs.readtools.documentation" target="classFrame">RTHelpDoclet</a></li>

diff --git a/docs/javadoc/allclasses-noframe.html b/docs/javadoc/allclasses-noframe.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Fri Jul 27 18:06:33 GMT 2018 -->
-<title>All Classes (ReadTools 1.5.0 API)</title>
-<meta name="date" content="2018-07-27">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
 <body>
 <h1 class="bar">All&nbsp;Classes</h1>
 <div class="indexContainer">
 <ul>
-<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>
+<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>
 <li><a href="org/magicdgs/readtools/tools/barcodes/AssignReadGroupByBarcode.html" title="class in org.magicdgs.readtools.tools.barcodes">AssignReadGroupByBarcode</a></li>
 <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>
 <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>
 <li><a href="org/magicdgs/readtools/cmd/programgroups/RTConversionProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups">RTConversionProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/engine/RTDataSource.html" title="class in org.magicdgs.readtools.engine">RTDataSource</a></li>
 <li><a href="org/magicdgs/readtools/RTDefaults.html" title="class in org.magicdgs.readtools">RTDefaults</a></li>
-<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html" title="class in org.magicdgs.readtools.utils.fastq">RTFastqContstants</a></li>
+<li><a href="org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html" title="class in org.magicdgs.readtools.cmd">RTDeprecatedToolsRegistry</a></li>
+<li><a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html" title="class in org.magicdgs.readtools.utils.fastq">RTFastqConstants</a></li>
 <li><a href="org/magicdgs/readtools/documentation/RTGSONWorkUnit.html" title="class in org.magicdgs.readtools.documentation">RTGSONWorkUnit</a></li>
 <li><a href="org/magicdgs/readtools/RTHelpConstants.html" title="class in org.magicdgs.readtools">RTHelpConstants</a></li>
 <li><a href="org/magicdgs/readtools/documentation/RTHelpDoclet.html" title="class in org.magicdgs.readtools.documentation">RTHelpDoclet</a></li>

diff --git a/docs/javadoc/constant-values.html b/docs/javadoc/constant-values.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Fri Jul 27 18:06:33 GMT 2018 -->
-<title>Constant Field Values (ReadTools 1.5.0 API)</title>
-<meta name="date" content="2018-07-27">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Constant Field Values (ReadTools 1.5.0 API)";
+            parent.document.title="Constant Field Values (ReadTools 1.5.1 API)";
         }
     }
     catch(err) {
@@ -965,18 +965,18 @@ <h2 title="org.magicdgs">org.magicdgs.*</h2>
 <ul class="blockList">
 <li class="blockList">
 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
-<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>
+<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>
 <tr>
 <th class="colFirst" scope="col">Modifier and Type</th>
 <th scope="col">Constant Field</th>
 <th class="colLast" scope="col">Value</th>
 </tr>
 <tbody>
 <tr class="altColor">
-<td class="colFirst"><a name="org.magicdgs.readtools.utils.fastq.RTFastqContstants.ILLUMINA_NAME_BARCODE_DELIMITER">
+<td class="colFirst"><a name="org.magicdgs.readtools.utils.fastq.RTFastqConstants.ILLUMINA_NAME_BARCODE_DELIMITER">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
-<td><code><a href="org/magicdgs/readtools/utils/fastq/RTFastqContstants.html#ILLUMINA_NAME_BARCODE_DELIMITER">ILLUMINA_NAME_BARCODE_DELIMITER</a></code></td>
+<td><code><a href="org/magicdgs/readtools/utils/fastq/RTFastqConstants.html#ILLUMINA_NAME_BARCODE_DELIMITER">ILLUMINA_NAME_BARCODE_DELIMITER</a></code></td>
 <td class="colLast"><code>"#"</code></td>
 </tr>
 </tbody>

diff --git a/docs/javadoc/deprecated-list.html b/docs/javadoc/deprecated-list.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Fri Jul 27 18:06:33 GMT 2018 -->
-<title>Deprecated List (ReadTools 1.5.0 API)</title>
-<meta name="date" content="2018-07-27">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Deprecated List (ReadTools 1.5.0 API)";
+            parent.document.title="Deprecated List (ReadTools 1.5.1 API)";
         }
     }
     catch(err) {

diff --git a/docs/javadoc/help-doc.html b/docs/javadoc/help-doc.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Fri Jul 27 18:06:33 GMT 2018 -->
-<title>API Help (ReadTools 1.5.0 API)</title>
-<meta name="date" content="2018-07-27">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="API Help (ReadTools 1.5.0 API)";
+            parent.document.title="API Help (ReadTools 1.5.1 API)";
         }
     }
     catch(err) {