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biopet.biopet
Commits
2fc77904
Commit
2fc77904
authored
Jan 23, 2017
by
Peter van 't Hof
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Adding licence to code
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+631
-0
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
+14
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
.../main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
+14
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
+14
-0
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
...t/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
+14
-0
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
.../nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
+14
-0
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.py
...ces/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.py
+15
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
...l/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
...sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
...nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
...main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
...cala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
...umc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
...a/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
...n/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
+14
-0
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
...est/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
+14
-0
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
.../test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
+14
-0
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
...scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
+14
-0
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
...cala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
...in/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleStats.scala
...cala/nl/lumc/sasc/biopet/tools/vcfstats/SampleStats.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleToSampleStats.scala
...lumc/sasc/biopet/tools/vcfstats/SampleToSampleStats.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
.../nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatchTest.scala
...cala/nl/lumc/sasc/biopet/tools/FindOverlapMatchTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateVcfTest.scala
...est/scala/nl/lumc/sasc/biopet/tools/ValidateVcfTest.scala
+14
-0
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/FastaUtils.scala
...src/main/scala/nl/lumc/sasc/biopet/utils/FastaUtils.scala
+14
-0
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala
...s/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala
+14
-0
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
.../src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
+14
-0
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/VcfUtilsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/utils/VcfUtilsTest.scala
+14
-0
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
...nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
+14
-0
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
...sc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+14
-0
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
...lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
+14
-0
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
...c/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
+14
-0
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
...umc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
+14
-0
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/template/MultiSampleMapping.scala
...iopet/pipelines/mapping/template/MultiSampleMapping.scala
+14
-0
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
+14
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
+14
-0
No files found.
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
2fc77904
/**
* 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.basty
import
java.io.
{
File
,
FileOutputStream
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
View file @
2fc77904
/**
* 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.core
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
View file @
2fc77904
/**
* 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.core
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
View file @
2fc77904
/**
* 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.core
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
View file @
2fc77904
/**
* 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.core.annotation
import
java.io.File
...
...
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.py
View file @
2fc77904
#
# 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.
#
import
argparse
from
os.path
import
join
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
View file @
2fc77904
/**
* 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-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
View file @
2fc77904
/**
* 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-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
2fc77904
/**
* 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.centrifuge
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
View file @
2fc77904
/**
* 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.centrifuge
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
2fc77904
/**
* 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.gatk
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
View file @
2fc77904
/**
* 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.xhmm
import
java.io.File
...
...
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
View file @
2fc77904
/**
* 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
org.scalatest.Matchers
...
...
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
View file @
2fc77904
/**
* 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-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
View file @
2fc77904
/**
* 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.tools
import
java.io.File
...
...
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
View file @
2fc77904
/**
* 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.tools
import
java.io.File
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
View file @
2fc77904
/**
* 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
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
View file @
2fc77904
/**
* 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
import
java.io.File
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
View file @
2fc77904
/**
* 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
import
java.io.
{
File
,
PrintStream
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
View file @
2fc77904
/**
* 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
import
java.io.File
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
View file @
2fc77904
/**
* 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
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
,
PrintWriter
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleStats.scala
View file @
2fc77904
/**
* 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.vcfstats
import
scala.collection.mutable
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleToSampleStats.scala
View file @
2fc77904
/**
* 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.vcfstats
/**
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
View file @
2fc77904
/**
* 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.vcfstats
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
View file @
2fc77904
/**
* 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