Release 1.5.2 (#529)

* Release javadoc * Release documentation site * Update CHANGELOG
magicDGS · Aug 30, 2018 · 92e3f40 · 92e3f40
1 parent c941838
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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]
 
+
+## [1.5.2]
+
 ### Fixed
 - Allow special characters in advance java-property for barcode sequence/quality separators
 
@@ -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
diff --git a/docs/_data/index.yml b/docs/_data/index.yml
@@ -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

diff --git a/docs/javadoc/allclasses-frame.html b/docs/javadoc/allclasses-frame.html
@@ -2,9 +2,9 @@
 <!-- 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>

diff --git a/docs/javadoc/allclasses-noframe.html b/docs/javadoc/allclasses-noframe.html
@@ -2,9 +2,9 @@
 <!-- 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>

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 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">
 <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 1.5.1 API)";
+            parent.document.title="Constant Field Values (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

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 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>
+<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>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Deprecated List (ReadTools 1.5.1 API)";
+            parent.document.title="Deprecated List (ReadTools 1.5.2 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 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>
 </head>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="API Help (ReadTools 1.5.1 API)";
+            parent.document.title="API Help (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/docs/javadoc/index-all.html b/docs/javadoc/index-all.html
@@ -2,17 +2,17 @@
 <!-- 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>
 </head>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Index (ReadTools 1.5.1 API)";
+            parent.document.title="Index (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
@@ -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>
@@ -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">
@@ -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>

diff --git a/docs/javadoc/index.html b/docs/javadoc/index.html
@@ -2,8 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <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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diff --git a/docs/javadoc/org/magicdgs/readtools/Main.html b/docs/javadoc/org/magicdgs/readtools/Main.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
-<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">
 <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="Main (ReadTools 1.5.1 API)";
+            parent.document.title="Main (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/docs/javadoc/org/magicdgs/readtools/RTDefaults.html b/docs/javadoc/org/magicdgs/readtools/RTDefaults.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
-<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">
 <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="RTDefaults (ReadTools 1.5.1 API)";
+            parent.document.title="RTDefaults (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/docs/javadoc/org/magicdgs/readtools/RTHelpConstants.html b/docs/javadoc/org/magicdgs/readtools/RTHelpConstants.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
-<title>RTHelpConstants (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>RTHelpConstants (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>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTHelpConstants (ReadTools 1.5.1 API)";
+            parent.document.title="RTHelpConstants (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html b/docs/javadoc/org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
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-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTDeprecatedToolsRegistry (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>RTDeprecatedToolsRegistry (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>
 <body>
 <script type="text/javascript"><!--
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         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTDeprecatedToolsRegistry (ReadTools 1.5.1 API)";
+            parent.document.title="RTDeprecatedToolsRegistry (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/RTStandardArguments.html b/docs/javadoc/org/magicdgs/readtools/cmd/RTStandardArguments.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
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-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTStandardArguments (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>RTStandardArguments (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>
 <body>
 <script type="text/javascript"><!--
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         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTStandardArguments (ReadTools 1.5.1 API)";
+            parent.document.title="RTStandardArguments (ReadTools 1.5.2 API)";
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diff --git a/...doc/org/magicdgs/readtools/cmd/argumentcollections/BarcodeDetectorArgumentCollection.html b/...doc/org/magicdgs/readtools/cmd/argumentcollections/BarcodeDetectorArgumentCollection.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>BarcodeDetectorArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>BarcodeDetectorArgumentCollection (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>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="BarcodeDetectorArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="BarcodeDetectorArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/...tions/FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection.html b/...tions/FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (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>
 <body>
 <script type="text/javascript"><!--
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         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/...tcollections/FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection.html b/...tcollections/FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (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>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {

diff --git a/.../org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.html b/.../org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.html
@@ -2,17 +2,17 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>FixBarcodeAbstractArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>FixBarcodeAbstractArgumentCollection (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>
 <body>
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="FixBarcodeAbstractArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="FixBarcodeAbstractArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {