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biopet.biopet
Commits
9cd4ef52
Commit
9cd4ef52
authored
Feb 14, 2017
by
Peter van 't Hof
Browse files
Moved class
parent
825998c2
Changes
5
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
9cd4ef52
...
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@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils.summary.SummaryDb
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils.summary.
db.
SummaryDb
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.QScript
import
scala.concurrent.Await
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
9cd4ef52
...
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@@ -14,11 +14,11 @@
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.utils.summary.SummaryDb
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.utils.summary.
db.
SummaryDb
import
org.broadinstitute.gatk.queue.QScript
import
scala.collection.mutable
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
9cd4ef52
...
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@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.LastCommitHash
import
nl.lumc.sasc.biopet.utils.summary.SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.
db.
SummaryDb
import
org.broadinstitute.gatk.queue.function.
{
InProcessFunction
,
QFunction
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
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...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
View file @
9cd4ef52
...
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@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
nl.lumc.sasc.biopet.utils.summary.SummaryDb
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.summary.
db.
SummaryDb
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
import
slick.driver.H2Driver.api._
import
scala.concurrent.Await
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryDb.scala
→
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/
db/
SummaryDb.scala
View file @
9cd4ef52
package
nl.lumc.sasc.biopet.utils.summary
package
nl.lumc.sasc.biopet.utils.summary
.db
import
java.io.
{
Closeable
,
File
}
import
java.io.
{
Closeable
,
File
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.summary.db.Schema
import
slick.driver.H2Driver.api._
import
scala.concurrent.
{
Await
,
Future
}
import
scala.concurrent.duration.Duration
import
nl.lumc.sasc.biopet.utils.summary.db.Schema._
import
slick.driver.H2Driver.api._
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.duration.Duration
import
scala.concurrent.
{
Await
,
Future
}
/**
* Created by pjvanthof on 05/02/2017.
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