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biopet.biopet
Commits
dd4f0175
Commit
dd4f0175
authored
Jul 29, 2014
by
Peter van 't Hof
Browse files
changed function to extensions
parent
8e67bf4f
Changes
37
Hide whitespace changes
Inline
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bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
dd4f0175
...
...
@@ -6,9 +6,9 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import
java.io.File
import
nl.lumc.sasc.biopet.core.apps.
{
BedToInterval
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.
funct
ion.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.
funct
ion.picard.
{
CollectInsertSizeMetrics
,
CollectGcBiasMetrics
,
CalculateHsMetrics
,
CollectAlignmentSummaryMetrics
}
import
nl.lumc.sasc.biopet.
funct
ion.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.
extens
ion
s
.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.
extens
ion
s
.picard.
{
CollectInsertSizeMetrics
,
CollectGcBiasMetrics
,
CalculateHsMetrics
,
CollectAlignmentSummaryMetrics
}
import
nl.lumc.sasc.biopet.
extens
ion
s
.samtools.SamtoolsFlagstat
class
BamMetrics
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.
funct
ion.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.
extens
ion
s
.PythonCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/Cat.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/Cat.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/Ln.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/Ln.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.function.InProcessFunction
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/Pbzip2.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/Pbzip2.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/PythonCommandLineFunction.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/PythonCommandLineFunction.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
java.io.FileOutputStream
import
java.io.File
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/Seqtk.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/Seqtk.scala
View file @
dd4f0175
...
...
@@ -4,7 +4,7 @@
* @author Wibowo Arindrarto
*/
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
java.io.File
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/Sha1sum.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/Sha1sum.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/Zcat.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/Zcat.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion
package
nl.lumc.sasc.biopet.
extens
ion
s
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/bedtools/Bedtools.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/bedtools/Bedtools.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.bedtools
package
nl.lumc.sasc.biopet.
extens
ion
s
.bedtools
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/bedtools/BedtoolsCoverage.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/bedtools/BedtoolsCoverage.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.bedtools
package
nl.lumc.sasc.biopet.
extens
ion
s
.bedtools
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/bedtools/BedtoolsIntersect.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/bedtools/BedtoolsIntersect.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.bedtools
package
nl.lumc.sasc.biopet.
extens
ion
s
.bedtools
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/picard/CalculateHsMetrics.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/picard/CalculateHsMetrics.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.picard
package
nl.lumc.sasc.biopet.
extens
ion
s
.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/picard/CollectAlignmentSummaryMetrics.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/picard/CollectAlignmentSummaryMetrics.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.picard
package
nl.lumc.sasc.biopet.
extens
ion
s
.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/picard/CollectGcBiasMetrics.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/picard/CollectGcBiasMetrics.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.picard
package
nl.lumc.sasc.biopet.
extens
ion
s
.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/picard/CollectInsertSizeMetrics.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/picard/CollectInsertSizeMetrics.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.picard
package
nl.lumc.sasc.biopet.
extens
ion
s
.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/picard/MarkDuplicates.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/picard/MarkDuplicates.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.picard
package
nl.lumc.sasc.biopet.
extens
ion
s
.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/picard/Picard.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/picard/Picard.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.picard
package
nl.lumc.sasc.biopet.
extens
ion
s
.picard
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/samtools/Samtools.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/samtools/Samtools.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.samtools
package
nl.lumc.sasc.biopet.
extens
ion
s
.samtools
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
funct
ion/samtools/SamtoolsFlagstat.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
extens
ion
s
/samtools/SamtoolsFlagstat.scala
View file @
dd4f0175
package
nl.lumc.sasc.biopet.
funct
ion.samtools
package
nl.lumc.sasc.biopet.
extens
ion
s
.samtools
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
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