Commit 95e63289 authored by Peter van 't Hof's avatar Peter van 't Hof

Removed indelrealignment from library level

parent 9c692ecf
...@@ -74,7 +74,10 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -74,7 +74,10 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
/** Sample specific settings */ /** Sample specific settings */
override def summarySettings: Map[String, Any] = super.summarySettings ++ override def summarySettings: Map[String, Any] = super.summarySettings ++
Map("single_sample_variantcalling" -> variantcalling.isDefined, "use_indel_realigner" -> useIndelRealigner) Map(
"single_sample_variantcalling" -> variantcalling.isDefined,
"use_indel_realigner" -> useIndelRealigner
)
/** Class to generate jobs for a library */ /** Class to generate jobs for a library */
class Library(libId: String) extends super.Library(libId) { class Library(libId: String) extends super.Library(libId) {
...@@ -84,7 +87,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -84,7 +87,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
bqsrFile.map("baserecal" -> _) ++ bqsrFile.map("baserecal" -> _) ++
bqsrAfterFile.map("baserecal_after" -> _) bqsrAfterFile.map("baserecal_after" -> _)
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
lazy val useBaseRecalibration: Boolean = { lazy val useBaseRecalibration: Boolean = {
val c: Boolean = config("use_base_recalibration", default = true) val c: Boolean = config("use_base_recalibration", default = true)
val br = new BaseRecalibrator(qscript) val br = new BaseRecalibrator(qscript)
...@@ -97,18 +99,15 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -97,18 +99,15 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
lazy val bqsrFile: Option[File] = if (useBaseRecalibration) Some(createFile("baserecal")) else None lazy val bqsrFile: Option[File] = if (useBaseRecalibration) Some(createFile("baserecal")) else None
lazy val bqsrAfterFile: Option[File] = if (useAnalyzeCovariates) Some(createFile("baserecal.after")) else None lazy val bqsrAfterFile: Option[File] = if (useAnalyzeCovariates) Some(createFile("baserecal.after")) else None
override def keepFinalBamfile: Boolean = super.keepFinalBamfile && !useIndelRealigner && !useBaseRecalibration override def keepFinalBamfile: Boolean = super.keepFinalBamfile && !useBaseRecalibration && !usePrintReads
override def preProcessBam: Option[Mapping#File] = if (useIndelRealigner && usePrintReads && useBaseRecalibration) override def preProcessBam: Option[Mapping#File] = if (usePrintReads && useBaseRecalibration)
bamFile.map(swapExt(libDir, _, ".bam", ".realign.baserecal.bam")) bamFile.map(swapExt(libDir, _, ".bam", ".baserecal.bam"))
else if (useIndelRealigner) bamFile.map(swapExt(libDir, _, ".bam", ".realign.bam"))
else if (usePrintReads && useBaseRecalibration) bamFile.map(swapExt(libDir, _, ".bam", ".baserecal.bam"))
else bamFile else bamFile
/** Library specific settings */ /** Library specific settings */
override def summarySettings: Map[String, Any] = super.summarySettings ++ Map( override def summarySettings: Map[String, Any] = super.summarySettings ++ Map(
"library_variantcalling" -> variantcalling.isDefined, "library_variantcalling" -> variantcalling.isDefined,
"use_indel_realigner" -> useIndelRealigner,
"use_base_recalibration" -> useBaseRecalibration, "use_base_recalibration" -> useBaseRecalibration,
"useAnalyze_covariates" -> useAnalyzeCovariates "useAnalyze_covariates" -> useAnalyzeCovariates
) )
...@@ -122,12 +121,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -122,12 +121,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
override def addJobs(): Unit = { override def addJobs(): Unit = {
super.addJobs() super.addJobs()
if (useIndelRealigner && useBaseRecalibration) { if (useBaseRecalibration) {
val file = addIndelRealign(bamFile.get, libDir, isIntermediate = true)
addBaseRecalibrator(file, libDir, libraries.size > 1, usePrintReads)
} else if (useIndelRealigner) {
addIndelRealign(bamFile.get, libDir, libraries.size > 1)
} else if (useBaseRecalibration) {
addBaseRecalibrator(bamFile.get, libDir, libraries.size > 1, usePrintReads) addBaseRecalibrator(bamFile.get, libDir, libraries.size > 1, usePrintReads)
} }
...@@ -195,7 +189,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -195,7 +189,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
override def addJobs(): Unit = { override def addJobs(): Unit = {
super.addJobs() super.addJobs()
if (useIndelRealigner && libraries.values.flatMap(_.preProcessBam).size > 1) { if (useIndelRealigner) {
addIndelRealign(bamFile.get, sampleDir, isIntermediate = false) addIndelRealign(bamFile.get, sampleDir, isIntermediate = false)
} }
......
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