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

a4c324e1 · Wai Yi Leung · ee32217c · bfdad518 · a4c324e1 · a4c324e1
Commit a4c324e1 authored May 31, 2016 by Wai Yi Leung
--- a/bam2wig/pom.xml
+++ b/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.


--- a/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/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.
 */

--- a/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+++ b/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.
 */

--- a/bam2wig/src/test/resources/log4j.properties
+++ b/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.
 #

--- a/bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
+++ b/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

--- a/bammetrics/pom.xml
+++ b/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.


--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
+++ b/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

--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
+++ b/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.
 #

--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/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.
 */

--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/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.
 */

--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
+++ b/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.
 */

--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+++ b/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.
 */

--- a/bammetrics/src/test/resources/log4j.properties
+++ b/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.
 #

--- a/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+++ b/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.
 */

--- a/basty/pom.xml
+++ b/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.


--- a/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/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.
 */

--- a/basty/src/test/resources/log4j.properties
+++ b/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.
 #

--- a/biopet-aggregate/pom.xml
+++ b/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">

--- a/biopet-core/pom.xml
+++ b/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.


--- a/biopet-core/src/main/resources/log4j.properties
+++ b/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.
 #