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biopet.biopet
Commits
2a3db002
Commit
2a3db002
authored
Aug 25, 2016
by
Peter van 't Hof
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Fixed licence headers
parent
6542c2db
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-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
+14
-0
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
...l/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
...ala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
...scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
...la/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
+14
-0
docs/examples/pom.xml
docs/examples/pom.xml
+16
-0
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
...mc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
+14
-0
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
...asc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
+14
-0
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
...elines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
+14
-0
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
...
...
docs/examples/pom.xml
View file @
2a3db002
<?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"
>
...
...
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
View file @
2a3db002
/**
* 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
View file @
2a3db002
/**
* 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
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
View file @
2a3db002
/**
* 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
...
...
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