magicDGS · magicDGS · Apr 25, 2018 · Apr 25, 2018 · Apr 25, 2018 · Apr 25, 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]
 
+
+## [1.3.0]
+
 ### Fixed
 - Fix failing uncompression of the jar file on OSX due to name collisions
 - More concise repository README without redundant information
@@ -227,3 +230,4 @@ First pre-release
 [1.1.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.1.0
 [1.2.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.2.0
 [1.2.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.2.1
+[1.3.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.3.0
diff --git a/docs/_data/index.yml b/docs/_data/index.yml
@@ -1,6 +1,6 @@
 ReadTools:
-  version: 1.2.1
-  timestamp: 02-17-2018 10:17:07
+  version: 1.3.0
+  timestamp: 25-37-2018 02:37:45
 
 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_60) on Fri Feb 02 10:17:05 CET 2018 -->
-<title>All Classes (ReadTools 1.2.1 API)</title>
-<meta name="date" content="2018-02-02">
+<!-- Generated by javadoc (1.8.0_60) on Wed Apr 25 14:37:40 CEST 2018 -->
+<title>All Classes (ReadTools 1.3.0 API)</title>
+<meta name="date" content="2018-04-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -40,6 +40,7 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/barcodes/FixRawBarcodeTagsReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer.barcodes" target="classFrame">FixRawBarcodeTagsReadTransformer</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/barcodes/FixReadNameBarcodesReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer.barcodes" target="classFrame">FixReadNameBarcodesReadTransformer</a></li>
 <li><a href="org/magicdgs/readtools/utils/iterators/paired/GATKReadPairedIterator.html" title="class in org.magicdgs.readtools.utils.iterators.paired" target="classFrame">GATKReadPairedIterator</a></li>
+<li><a href="org/magicdgs/readtools/utils/HadoopUtils.html" title="class in org.magicdgs.readtools.utils" target="classFrame">HadoopUtils</a></li>
 <li><a href="org/magicdgs/readtools/utils/iterators/InterleaveGATKReadIterators.html" title="class in org.magicdgs.readtools.utils.iterators" target="classFrame">InterleaveGATKReadIterators</a></li>
 <li><a href="org/magicdgs/readtools/Main.html" title="class in org.magicdgs.readtools" target="classFrame">Main</a></li>
 <li><a href="org/magicdgs/readtools/metrics/barcodes/MatcherStat.html" title="class in org.magicdgs.readtools.metrics.barcodes" target="classFrame">MatcherStat</a></li>

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_60) on Fri Feb 02 10:17:05 CET 2018 -->
-<title>All Classes (ReadTools 1.2.1 API)</title>
-<meta name="date" content="2018-02-02">
+<!-- Generated by javadoc (1.8.0_60) on Wed Apr 25 14:37:40 CEST 2018 -->
+<title>All Classes (ReadTools 1.3.0 API)</title>
+<meta name="date" content="2018-04-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -40,6 +40,7 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/barcodes/FixRawBarcodeTagsReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer.barcodes">FixRawBarcodeTagsReadTransformer</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/barcodes/FixReadNameBarcodesReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer.barcodes">FixReadNameBarcodesReadTransformer</a></li>
 <li><a href="org/magicdgs/readtools/utils/iterators/paired/GATKReadPairedIterator.html" title="class in org.magicdgs.readtools.utils.iterators.paired">GATKReadPairedIterator</a></li>
+<li><a href="org/magicdgs/readtools/utils/HadoopUtils.html" title="class in org.magicdgs.readtools.utils">HadoopUtils</a></li>
 <li><a href="org/magicdgs/readtools/utils/iterators/InterleaveGATKReadIterators.html" title="class in org.magicdgs.readtools.utils.iterators">InterleaveGATKReadIterators</a></li>
 <li><a href="org/magicdgs/readtools/Main.html" title="class in org.magicdgs.readtools">Main</a></li>
 <li><a href="org/magicdgs/readtools/metrics/barcodes/MatcherStat.html" title="class in org.magicdgs.readtools.metrics.barcodes">MatcherStat</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_60) on Fri Feb 02 10:17:04 CET 2018 -->
-<title>Constant Field Values (ReadTools 1.2.1 API)</title>
-<meta name="date" content="2018-02-02">
+<!-- Generated by javadoc (1.8.0_60) on Wed Apr 25 14:37:40 CEST 2018 -->
+<title>Constant Field Values (ReadTools 1.3.0 API)</title>
+<meta name="date" content="2018-04-25">
 <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 1.2.1 API)";
+            parent.document.title="Constant Field Values (ReadTools 1.3.0 API)";
         }
     }
     catch(err) {
@@ -447,174 +447,181 @@ <h2 title="org.magicdgs">org.magicdgs.*</h2>
 <td class="colLast"><code>"splitReadGroup"</code></td>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.READ_VALIDATION_STRINGENCY_DOC">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
+<td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#READ_VALIDATION_STRINGENCY_DOC">READ_VALIDATION_STRINGENCY_DOC</a></code></td>
+<td class="colLast"><code>"Validation stringency for all SAM/BAM/CRAM files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."</code></td>
+</tr>
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.READ_VALIDATION_STRINGENCY_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#READ_VALIDATION_STRINGENCY_LONG_NAME">READ_VALIDATION_STRINGENCY_LONG_NAME</a></code></td>
 <td class="colLast"><code>"readValidationStringency"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.READ_VALIDATION_STRINGENCY_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#READ_VALIDATION_STRINGENCY_SHORT_NAME">READ_VALIDATION_STRINGENCY_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"VS"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.REFERENCE_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#REFERENCE_LONG_NAME">REFERENCE_LONG_NAME</a></code></td>
 <td class="colLast"><code>"reference"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.REFERENCE_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#REFERENCE_SHORT_NAME">REFERENCE_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"R"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGCN_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGCN_LONG_NAME">RGCN_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGCN"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGCN_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGCN_SHORT_NAME">RGCN_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"CN"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGDT_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGDT_LONG_NAME">RGDT_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGDT"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGDT_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGDT_SHORT_NAME">RGDT_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"DT"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGLB_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGLB_LONG_NAME">RGLB_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGLB"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGLB_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGLB_SHORT_NAME">RGLB_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"LB"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPI_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPI_LONG_NAME">RGPI_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGPI"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPI_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPI_SHORT_NAME">RGPI_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"PI"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPL_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPL_LONG_NAME">RGPL_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGPL"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPL_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPL_SHORT_NAME">RGPL_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"PL"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPM_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPM_LONG_NAME">RGPM_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGPM"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPM_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPM_SHORT_NAME">RGPM_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"PM"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPU_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPU_LONG_NAME">RGPU_LONG_NAME</a></code></td>
 <td class="colLast"><code>"RGPU"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.RGPU_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#RGPU_SHORT_NAME">RGPU_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"PU"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.SAMPLE_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#SAMPLE_LONG_NAME">SAMPLE_LONG_NAME</a></code></td>
 <td class="colLast"><code>"splitSample"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.SECONDS_BETWEEN_PROGRESS_UPDATES_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#SECONDS_BETWEEN_PROGRESS_UPDATES_NAME">SECONDS_BETWEEN_PROGRESS_UPDATES_NAME</a></code></td>
 <td class="colLast"><code>"secondsBetweenProgressUpdates"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.SORT_ORDER_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#SORT_ORDER_LONG_NAME">SORT_ORDER_LONG_NAME</a></code></td>
 <td class="colLast"><code>"SORT_ORDER"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.SORT_ORDER_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#SORT_ORDER_SHORT_NAME">SORT_ORDER_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"SO"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.TRIMMER_LONG_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#TRIMMER_LONG_NAME">TRIMMER_LONG_NAME</a></code></td>
 <td class="colLast"><code>"trimmer"</code></td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.TRIMMER_SHORT_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 <td><code><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html#TRIMMER_SHORT_NAME">TRIMMER_SHORT_NAME</a></code></td>
 <td class="colLast"><code>"TM"</code></td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.cmd.RTStandardArguments.USER_READ_NAME_BARCODE_NAME">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>

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_60) on Fri Feb 02 10:17:05 CET 2018 -->
-<title>Deprecated List (ReadTools 1.2.1 API)</title>
-<meta name="date" content="2018-02-02">
+<!-- Generated by javadoc (1.8.0_60) on Wed Apr 25 14:37:40 CEST 2018 -->
+<title>Deprecated List (ReadTools 1.3.0 API)</title>
+<meta name="date" content="2018-04-25">
 <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 1.2.1 API)";
+            parent.document.title="Deprecated List (ReadTools 1.3.0 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_60) on Fri Feb 02 10:17:05 CET 2018 -->
-<title>API Help (ReadTools 1.2.1 API)</title>
-<meta name="date" content="2018-02-02">
+<!-- Generated by javadoc (1.8.0_60) on Wed Apr 25 14:37:40 CEST 2018 -->
+<title>API Help (ReadTools 1.3.0 API)</title>
+<meta name="date" content="2018-04-25">
 <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 1.2.1 API)";
+            parent.document.title="API Help (ReadTools 1.3.0 API)";
         }
     }
     catch(err) {