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biopet.biopet
Commits
5a7b30eb
Commit
5a7b30eb
authored
Aug 26, 2016
by
Peter van 't Hof
Browse files
Merge remote-tracking branch 'remotes/origin/release-0.7.0' into develop
parents
2a6a08ee
e8783392
Changes
41
Hide whitespace changes
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bam2wig/pom.xml
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
...
...
@@ -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
View file @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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 @
5a7b30eb
/**
* 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
...
...
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