From 091f86da75fb56f3e2bb42f9fc019eb8c0386615 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 9 Jan 2015 15:40:44 +0100
Subject: [PATCH] Extended sample handing in multisample qscript
---
.../biopet/pipelines/gatk/GatkPipeline.scala | 4 +-
.../sasc/biopet/core/MultiSampleQScript.scala | 51 ++++++++++++++++++-
.../lumc/sasc/biopet/core/ToolCommand.scala | 8 +--
.../biopet/core/config/Configurable.scala | 6 +--
.../lumc/sasc/biopet/utils/ConfigUtils.scala | 1 +
5 files changed, 60 insertions(+), 10 deletions(-)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 75834b45f..0031e2c15 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -62,7 +62,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
val multisampleVariantcalling = new GatkVariantcalling(this) {
- override protected lazy val configName = "gatkvariantcalling"
+ override def configName = "gatkvariantcalling"
override def configPath: List[String] = "multisample" :: super.configPath
}
@@ -97,7 +97,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val allRawVcfFiles = for ((sampleID, sampleOutput) <- samplesOutput) yield sampleOutput.variantcalling.rawFilterVcfFile
val gatkVariantcalling = new GatkVariantcalling(this) {
- override protected lazy val configName = "gatkvariantcalling"
+ override def configName = "gatkvariantcalling"
override def configPath: List[String] = "multisample" :: super.configPath
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index bfce62da0..3eb4fc516 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.core
-import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
+import nl.lumc.sasc.biopet.core.config.{ ConfigValue, Config, Configurable }
import nl.lumc.sasc.biopet.utils.ConfigUtils._
trait MultiSampleQScript extends BiopetQScript {
@@ -39,7 +39,9 @@ trait MultiSampleQScript extends BiopetQScript {
var sample = any2map(value)
if (!sample.contains("ID")) sample += ("ID" -> key)
if (sample("ID") == key) {
+ setCurrentSample(key)
samplesOutput += key -> runSingleSampleJobs(sample)
+ unsetCurrentSample()
} else logger.warn("Key is not the same as ID on value for sample")
}
else logger.warn("No Samples found in config")
@@ -63,11 +65,58 @@ trait MultiSampleQScript extends BiopetQScript {
var library = any2map(value)
if (!library.contains("ID")) library += ("ID" -> key)
if (library("ID") == key) {
+ setCurrentLibrary(key)
output += key -> runSingleLibraryJobs(library, sampleConfig)
+ unsetCurrentLibrary()
} else logger.warn("Key is not the same as ID on value for run of sample: " + sampleID)
}
} else logger.warn("No runs found in config for sample: " + sampleID)
return output
}
def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput
+
+ private var currentSample: String = null
+ private var currentLibrary: String = null
+
+ def setCurrentSample(sample: String) {
+ currentSample = sample
+ }
+
+ def unsetCurrentSample() {
+ currentSample = null
+ }
+
+ def setCurrentLibrary(library: String) {
+ currentLibrary = library
+ }
+
+ def unsetCurrentLibrary() {
+ currentLibrary = null
+ }
+
+ override protected[core] def configFullPath: List[String] = {
+ (if (currentSample != null) "samples" :: currentSample :: Nil else Nil) :::
+ (if (currentLibrary != null) "libraries" :: currentLibrary :: Nil else Nil) :::
+ super.configFullPath
+ }
+
+ protected class ConfigFunctions extends super.ConfigFunctions {
+ override def apply(key: String,
+ default: Any = null,
+ submodule: String = null,
+ required: Boolean = false,
+ freeVar: Boolean = true,
+ sample: String = currentSample,
+ library: String = currentLibrary): ConfigValue = {
+ super.apply(key, default, submodule, required, freeVar, sample, library)
+ }
+
+ override def contains(key: String,
+ submodule: String = null,
+ freeVar: Boolean = true,
+ sample: String = currentSample,
+ library: String = currentLibrary) = {
+ super.contains(key, submodule, freeVar, sample, library)
+ }
+ }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index c454c0a91..b3b25e9a7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -16,10 +16,10 @@
package nl.lumc.sasc.biopet.core
trait ToolCommand extends MainCommand with Logging {
- abstract class AbstractArgs {
+ protected abstract class AbstractArgs {
}
- abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
+ protected abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
opt[String]('l', "log_level") foreach { x =>
x.toLowerCase match {
case "debug" => logger.setLevel(org.apache.log4j.Level.DEBUG)
@@ -44,6 +44,6 @@ trait ToolCommand extends MainCommand with Logging {
} text ("Print version")
}
- type Args <: AbstractArgs
- type OptParser <: AbstractOptParser
+ protected type Args <: AbstractArgs
+ protected type OptParser <: AbstractOptParser
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 9ce006570..54c67437d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -21,9 +21,9 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
trait Configurable extends ImplicitConversions {
val root: Configurable
- lazy val configPath: List[String] = if (root != null) root.configFullPath else List()
- protected[config] lazy val configName = getClass.getSimpleName.toLowerCase
- protected[config] lazy val configFullPath: List[String] = configPath ::: configName :: Nil
+ def configPath: List[String] = if (root != null) root.configFullPath else List()
+ protected[core] def configName = getClass.getSimpleName.toLowerCase
+ protected[core] def configFullPath: List[String] = configPath ::: configName :: Nil
var defaults: scala.collection.mutable.Map[String, Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray: _*)
else scala.collection.mutable.Map()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 9855e7248..a0a428d60 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -200,6 +200,7 @@ object ConfigUtils extends Logging {
any match {
case i: Int => i
case i: Double => i.toInt
+ case i: Long => i.toInt
case i: String => {
logger.warn("Value '" + any + "' is a string insteadof int in json file, trying auto convert")
i.toInt
--
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