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biopet.biopet
Commits
5a381b3d
Commit
5a381b3d
authored
Sep 10, 2015
by
Peter van 't Hof
Browse files
Moving utils
parent
1028f4da
Changes
15
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
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5a381b3d
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.
{
PrintWriter
,
StringWriter
}
import
nl.lumc.sasc.biopet.core.BiopetExecutable._
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.
{
FullVersion
,
LastCommitHash
}
import
org.apache.log4j.Logger
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
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5a381b3d
...
...
@@ -19,6 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.QSettings
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
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5a381b3d
...
...
@@ -19,6 +19,7 @@ import java.io.{ File, PrintWriter }
import
nl.lumc.sasc.biopet.core.config.Config
import
nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
import
nl.lumc.sasc.biopet.utils.Logging
import
org.apache.log4j.
{
PatternLayout
,
WriterAppender
}
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
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5a381b3d
...
...
@@ -16,6 +16,7 @@
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.FullVersion
import
nl.lumc.sasc.biopet.utils.Logging
/**
* Trait for biopet tools, sets some default args
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
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5a381b3d
...
...
@@ -16,9 +16,7 @@
package
nl.lumc.sasc.biopet.core.config
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.Logging
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
ConfigUtils
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
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5a381b3d
...
...
@@ -18,8 +18,8 @@ package nl.lumc.sasc.biopet.core.report
import
java.io._
import
nl.lumc.sasc.biopet.core.summary.Summary
import
nl.lumc.sasc.biopet.core.
{
Logging
,
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.utils.IoUtils
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
IoUtils
}
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.fusesource.scalate.
{
TemplateEngine
,
TemplateSource
}
import
scala.collection.mutable
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
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5a381b3d
...
...
@@ -50,7 +50,7 @@ import java.util
import
java.util.ResourceBundle
import
nl.lumc.sasc.biopet.FullVersion
import
nl.lumc.sasc.biopet.
core
.Logging
import
nl.lumc.sasc.biopet.
utils
.Logging
import
org.broadinstitute.gatk.queue.engine.
{
QGraph
,
QGraphSettings
}
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
,
ScalaCompoundArgumentTypeDescriptor
,
ClassFieldCache
}
import
org.broadinstitute.gatk.queue.
{
QCommandPlugin
,
QScript
,
QScriptManager
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
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5a381b3d
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
Logging
}
import
nl.lumc.sasc.biopet.utils.tryToParseNumber
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
tryToParseNumber
}
import
org.broadinstitute.gatk.utils.commandline.Argument
import
scala.io.Source
...
...
public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
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5a381b3d
...
...
@@ -19,7 +19,8 @@ import java.io.File
import
argonaut.Argonaut._
import
argonaut._
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
Logging
}
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
}
import
nl.lumc.sasc.biopet.core.config.ConfigValue
import
org.yaml.snakeyaml.Yaml
...
...
public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
View file @
5a381b3d
File moved
public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/
core
/Logging.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/
utils
/Logging.scala
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5a381b3d
...
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@@ -13,7 +13,7 @@
* 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
package
nl.lumc.sasc.biopet.
utils
import
org.apache.log4j.Logger
...
...
public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
View file @
5a381b3d
File moved
public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
View file @
5a381b3d
File moved
public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
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5a381b3d
...
...
@@ -9,7 +9,7 @@ import scala.collection.JavaConversions._
import
scala.collection.mutable
import
scala.collection.mutable.ListBuffer
import
scala.io.Source
import
nl.lumc.sasc.biopet.
core
.Logging
import
nl.lumc.sasc.biopet.
utils
.Logging
/**
* Created by pjvan_thof on 8/20/15.
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public/biopet-
framework
/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
→
public/biopet-
utils
/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
View file @
5a381b3d
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