Merge remote-tracking branch 'remotes/origin/release-0.7.0' into develop

bam2wig/pom.xml

@@ -26,7 +26,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
 

bammetrics/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

basty/pom.xml

@@ -31,7 +31,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

biopet-core/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

biopet-extensions/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.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.extensions.bedtools
 
 import java.io.File

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.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.extensions.hisat
 
 import java.io.File

biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.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.extensions
 
 import java.io.File

biopet-package/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

biopet-tools-extensions/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

biopet-tools-package/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

biopet-tools/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

@@ -63,7 +63,7 @@ object ExtractAlignedFastq extends ToolCommand {
     def intFromCoord(s: String): Int = s.replaceAll(",", "").replaceAll("\\.", "").toInt
 
     inStrings.map {
-      case ptn1(chr, start, end) if intFromCoord(end) >= intFromCoord(start)  => new Interval(chr, intFromCoord(start), intFromCoord(end))
+      case ptn1(chr, start, end) if intFromCoord(end) >= intFromCoord(start) => new Interval(chr, intFromCoord(start), intFromCoord(end))
       case ptn2(chr, start) =>
         val startCoord = intFromCoord(start)
         new Interval(chr, startCoord, startCoord)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.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.tools.bamstats
 
 import java.io.File

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.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.tools.bamstats
 
 import java.io.{ File, PrintWriter }

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.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.tools.bamstats
 
 import java.io.File

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.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.tools.flagstat
 
 import java.io.{ File, PrintWriter }

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.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.tools.bamstats
 
 import java.io.File

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.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.tools.bamstats
 
 import java.io.File

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.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.tools.bamstats
 
 import java.io.File

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.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.tools.bamstats
 
 import org.scalatest.Matchers

biopet-utils/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

carp/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

docs/examples/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">
@@ -6,7 +22,7 @@
 
     <groupId>path.to.your</groupId>
     <artifactId>MyProject</artifactId>
-    <version>YourVersion1.0</version>
+    <version>0.8.0-SNAPSHOT</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

docs/releasenotes/release_notes_0.7.0.md

-# Release notes Biopet version 0.6.0
+# Release notes Biopet version 0.7.0
 
 ## General Code changes
 
@@ -24,6 +24,7 @@
 * Utils - BamUtils is now estimating insert size by sampling the bam-file taking all parts of the available contigs.
 * Fix in VCF filter (#370)[https://git.lumc.nl/biopet/biopet/merge_requests/370]
 * Fix Star wrapper - added full functionality in wrapper.
+* Added a new tools: BamStats
 
 ## Reporting
 

external-example/pom.xml

@@ -27,7 +27,7 @@
     <artifactId>ExternalExample</artifactId>
 
     <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
-    <version>0.7.0-SNAPSHOT</version>
+    <version>0.8.0-SNAPSHOT</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -56,19 +56,19 @@
             <artifactId>BiopetCore</artifactId>
 
             <!--TODO: replace version of pipeline to a fixed version -->
-            <version>0.7.0-SNAPSHOT</version>
+            <version>0.8.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>BiopetExtensions</artifactId>
-            <version>0.7.0-SNAPSHOT</version>
+            <version>0.8.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Shiva</artifactId>
 
             <!--TODO: replace version of pipeline to a fixed version -->
-            <version>0.7.0-SNAPSHOT</version>
+            <version>0.8.0-SNAPSHOT</version>
         </dependency>
     </dependencies>
 

flexiprep/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

gears/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

generate-indexes/pom.xml

@@ -26,7 +26,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
 

gentrap/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

gwas-test/pom.xml

@@ -26,7 +26,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
 

gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.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.gwastest.impute
 
 import java.io.File

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.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.gwastest.impute
 
 import java.io.File

kopisu/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

mapping/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

pom.xml

@@ -21,7 +21,7 @@
     <groupId>nl.lumc.sasc</groupId>
     <name>Biopet</name>
     <packaging>pom</packaging>
-    <version>0.7.0-SNAPSHOT</version>
+    <version>0.8.0-SNAPSHOT</version>
     
     <modules>
         <module>biopet-package</module>

sage/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
     

shiva/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.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.shiva.variantcallers
 
 import java.io.File

tinycap/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

toucan/pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.7.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>