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

bam2wig/pom.xml

@@ -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.
 

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -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.
  */

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

@@ -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.
  */

bam2wig/src/test/resources/log4j.properties

@@ -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.
 #

bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala

+/**
+ * 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

bammetrics/pom.xml

@@ -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.
 

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

@@ -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

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py

@@ -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.
 #

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -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.
  */

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -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.
  */

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala

@@ -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.
  */

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

@@ -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.
  */

bammetrics/src/test/resources/log4j.properties

@@ -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.
 #

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -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.
  */

basty/pom.xml

@@ -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.
 

basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -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.
  */

basty/src/test/resources/log4j.properties

@@ -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-aggregate/pom.xml

 <?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">

biopet-core/pom.xml

@@ -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.
 

biopet-core/src/main/resources/log4j.properties

@@ -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.
 #