magicDGS · magicDGS · Jul 27, 2018 · Jul 27, 2018 · Jul 27, 2018 · Jul 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]
 
+
+## [1.5.0]
+
 ### Fixed
 - Improved performance for quality checking in every tool
 - Improved performance for trimming pipelines
@@ -279,3 +282,4 @@ First pre-release
 [1.3.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.3.0
 [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
diff --git a/docs/_data/index.yml b/docs/_data/index.yml
@@ -1,6 +1,6 @@
 ReadTools:
-  version: 1.4.1
-  timestamp: 11-25-2018 03:25:45
+  version: 1.5.0
+  timestamp: 27-06-2018 06:06:39
 
 tools:
   - group: Diagnostics and Quality Control
@@ -18,6 +18,12 @@ tools:
       - name: ReadsToDistmap
         summary: Converts any kind of ReadTools source to Distmap format.
         status: 'null'
+  - group: Mappabilty
+    summary: Tools related with mappability on the genome
+    components:
+      - name: GemMappabilityToBed
+        summary: Converts a GEM-mappability file into a BED-graph format
+        status: '_**EXPERIMENTAL**_'
   - group: Mapped reads
     summary: Tools operating on already mapped reads (SAM/BAM/CRAM only)
     components:

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 Mon Jun 11 15:25:43 CEST 2018 -->
-<title>All Classes (ReadTools 1.4.1 API)</title>
-<meta name="date" content="2018-06-11">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -44,9 +44,16 @@ <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/mappability/gem/GemMappabilityException.html" title="class in org.magicdgs.readtools.utils.mappability.gem" target="classFrame">GemMappabilityException</a></li>
+<li><a href="org/magicdgs/readtools/utils/mappability/gem/GemMappabilityHeader.html" title="class in org.magicdgs.readtools.utils.mappability.gem" target="classFrame">GemMappabilityHeader</a></li>
+<li><a href="org/magicdgs/readtools/utils/mappability/gem/GemMappabilityReader.html" title="class in org.magicdgs.readtools.utils.mappability.gem" target="classFrame">GemMappabilityReader</a></li>
+<li><a href="org/magicdgs/readtools/utils/mappability/gem/GemMappabilityRecord.html" title="class in org.magicdgs.readtools.utils.mappability.gem" target="classFrame">GemMappabilityRecord</a></li>
+<li><a href="org/magicdgs/readtools/tools/mappability/gem/GemMappabilityToBed.html" title="class in org.magicdgs.readtools.tools.mappability.gem" target="classFrame">GemMappabilityToBed</a></li>
+<li><a href="org/magicdgs/readtools/tools/mappability/gem/GemScoreMethod.html" title="enum in org.magicdgs.readtools.tools.mappability.gem" target="classFrame">GemScoreMethod</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/cmd/programgroups/MappabiltityProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups" target="classFrame">MappabiltityProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/cmd/programgroups/MappedProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups" target="classFrame">MappedProgramGroup</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>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/MottQualityTrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">MottQualityTrimmer</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 Mon Jun 11 15:25:43 CEST 2018 -->
-<title>All Classes (ReadTools 1.4.1 API)</title>
-<meta name="date" content="2018-06-11">
+<!-- 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">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -44,9 +44,16 @@ <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/mappability/gem/GemMappabilityException.html" title="class in org.magicdgs.readtools.utils.mappability.gem">GemMappabilityException</a></li>
+<li><a href="org/magicdgs/readtools/utils/mappability/gem/GemMappabilityHeader.html" title="class in org.magicdgs.readtools.utils.mappability.gem">GemMappabilityHeader</a></li>
+<li><a href="org/magicdgs/readtools/utils/mappability/gem/GemMappabilityReader.html" title="class in org.magicdgs.readtools.utils.mappability.gem">GemMappabilityReader</a></li>
+<li><a href="org/magicdgs/readtools/utils/mappability/gem/GemMappabilityRecord.html" title="class in org.magicdgs.readtools.utils.mappability.gem">GemMappabilityRecord</a></li>
+<li><a href="org/magicdgs/readtools/tools/mappability/gem/GemMappabilityToBed.html" title="class in org.magicdgs.readtools.tools.mappability.gem">GemMappabilityToBed</a></li>
+<li><a href="org/magicdgs/readtools/tools/mappability/gem/GemScoreMethod.html" title="enum in org.magicdgs.readtools.tools.mappability.gem">GemScoreMethod</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/cmd/programgroups/MappabiltityProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups">MappabiltityProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/cmd/programgroups/MappedProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups">MappedProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/metrics/barcodes/MatcherStat.html" title="class in org.magicdgs.readtools.metrics.barcodes">MatcherStat</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/MottQualityTrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming">MottQualityTrimmer</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 Mon Jun 11 15:25:43 CEST 2018 -->
-<title>Constant Field Values (ReadTools 1.4.1 API)</title>
-<meta name="date" content="2018-06-11">
+<!-- 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">
 <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 1.4.1 API)";
+            parent.document.title="Constant Field Values (ReadTools 1.5.0 API)";
         }
     }
     catch(err) {
@@ -104,6 +104,20 @@ <h2 title="org.magicdgs">org.magicdgs.*</h2>
 <td class="colLast"><code>"Tools for integration with the DistMap (Pandey &amp; Schl\u00f6tterer 2013)."</code></td>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><a name="org.magicdgs.readtools.RTHelpConstants.DOC_CAT_MAPPABILITY">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
+<td><code><a href="org/magicdgs/readtools/RTHelpConstants.html#DOC_CAT_MAPPABILITY">DOC_CAT_MAPPABILITY</a></code></td>
+<td class="colLast"><code>"Mappabilty"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.magicdgs.readtools.RTHelpConstants.DOC_CAT_MAPPABILITY_SUMMARY">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
+<td><code><a href="org/magicdgs/readtools/RTHelpConstants.html#DOC_CAT_MAPPABILITY_SUMMARY">DOC_CAT_MAPPABILITY_SUMMARY</a></code></td>
+<td class="colLast"><code>"Tools related with mappability on the genome"</code></td>
+</tr>
+<tr class="altColor">
 <td class="colFirst"><a name="org.magicdgs.readtools.RTHelpConstants.DOC_CAT_MAPPED">
 <!--   -->
 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
@@ -888,6 +902,27 @@ <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.tools.mappability.gem.<a href="org/magicdgs/readtools/tools/mappability/gem/GemMappabilityToBed.html" title="class in org.magicdgs.readtools.tools.mappability.gem">GemMappabilityToBed</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.tools.mappability.gem.GemMappabilityToBed.SUMMARY">
+<!--   -->
+</a><code>protected&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
+<td><code><a href="org/magicdgs/readtools/tools/mappability/gem/GemMappabilityToBed.html#SUMMARY">SUMMARY</a></code></td>
+<td class="colLast"><code>"Converts a GEM-mappability file (Derrien et al. 2012) into a BED-graph format converting the number of mappings to different kind of scores.\nThe GEM-mappability format is a FASTA-like file with:\n\t- Header including information for the algorithm applied and encoding.\n\t- Sequences in a FASTA-like format representing number of mappings\nEach character encodes a different range of values, which represent the number of mappings of each base.\n\nFind more information about this tool in http://magicdgs.github.io/ReadTools/GemMappabilityToBed.html"</code></td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
+<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.tools.mapped.<a href="org/magicdgs/readtools/tools/mapped/ComputeProperStatByWindow.html" title="class in org.magicdgs.readtools.tools.mapped">ComputeProperStatByWindow</a></span><span class="tabEnd">&nbsp;</span></caption>
 <tr>
 <th class="colFirst" scope="col">Modifier and Type</th>

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 Mon Jun 11 15:25:43 CEST 2018 -->
-<title>Deprecated List (ReadTools 1.4.1 API)</title>
-<meta name="date" content="2018-06-11">
+<!-- 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">
 <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 1.4.1 API)";
+            parent.document.title="Deprecated List (ReadTools 1.5.0 API)";
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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 Mon Jun 11 15:25:43 CEST 2018 -->
-<title>API Help (ReadTools 1.4.1 API)</title>
-<meta name="date" content="2018-06-11">
+<!-- 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">
 <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 1.4.1 API)";
+            parent.document.title="API Help (ReadTools 1.5.0 API)";
         }
     }
     catch(err) {