Commit a4c324e1 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge remote-tracking branch 'origin/develop' into develop

parents ee32217c bfdad518
......@@ -10,8 +10,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import java.io.File
......
......@@ -9,8 +9,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
......
......@@ -63,6 +63,7 @@
#if (!sampleLevel) <th>Library</th> #end
<th>Total</th>
<th>Mapped</th>
<th>Secondary</th>
<th>(%)</th>
<th>Duplicates</th>
<th>(%)</th>
......@@ -85,12 +86,14 @@
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val secondary = summary.getValue((prefixPath ::: List("biopet_flagstat", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
<td>${mapped.toDouble / total * 100}%</td>
<td>${secondary}</td>
<td>${(mapped - secondary).toDouble / (total - secondary) * 100}%</td>
<td>${duplicates}</td>
<td>${duplicates.toDouble / total * 100}%</td>
<td>${duplicates.toDouble / (total - secondary) * 100}%</td>
</tr>
#end
#end
......
......@@ -9,8 +9,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -9,8 +9,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
......
......@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
......
......@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
......
<?xml version="1.0" encoding="UTF-8"?>
<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
......
......@@ -10,8 +10,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
......
......@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
......
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