Added nested class, configContains() now replaced by config.contains()

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -9,30 +9,31 @@ trait Configurable extends Logging {
   val configPath: List[String] = if (root != null) root.configFullPath else List()
   protected val configName = getClass.getSimpleName.toLowerCase
   protected val configFullPath = configName :: configPath
-
-  def config(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar:Boolean = true): ConfigValue = {
-    val m = if (submodule != null) submodule else configName
-    val p = if (submodule != null) configName :: configPath else configPath
-    if (!configContains(key, submodule, freeVar) && default == null) {
-      if (required) {
-        logger.error("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
-        throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
-      } else return null
+  
+  val config = new ConfigFuntions
+  
+  protected class ConfigFuntions {
+    def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar:Boolean = true): ConfigValue = {
+      val m = if (submodule != null) submodule else configName
+      val p = if (submodule != null) configName :: configPath else configPath
+      if (!contains(key, submodule, freeVar) && default == null) {
+        if (required) {
+          logger.error("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
+          throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
+        } else return null
+      }
+      if (default == null) return globalConfig(m, p, key, freeVar)
+      else return globalConfig(m, p, key, default, freeVar)
     }
-    if (default == null) return globalConfig(m, p, key, freeVar)
-    else return globalConfig(m, p, key, default, freeVar)
-  }
-  //def config(key:String, default:Any) = globalConfig(configName, configPath, key, default)
-  //def config(key:String, default:Any, module:String) = globalConfig(module, configName :: configPath, key, default)
+    
+    def contains(key: String, submodule: String = null, freeVar:Boolean = true) = {
+      val m = if (submodule != null) submodule else configName
+      val p = if (submodule != null) configName :: configPath else configPath
 
-  //def configContains(key:String) = globalConfig.contains(configName, configPath, key)
-  def configContains(key: String, submodule: String = null, freeVar:Boolean = true) = {
-    val m = if (submodule != null) submodule else configName
-    val p = if (submodule != null) configName :: configPath else configPath
-
-    globalConfig.contains(m, p, key, freeVar)
+      globalConfig.contains(m, p, key, freeVar)
+    }
   }
-
+  
   implicit def configValue2file(value: ConfigValue): File = if (value != null) new File(Configurable.any2string(value.value)) else null
   implicit def configValue2string(value: ConfigValue): String = if (value != null) Configurable.any2string(value.value) else null
   implicit def configValue2long(value: ConfigValue): Long = if (value != null) Configurable.any2long(value.value) else 0

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

 package nl.lumc.sasc.biopet.extensions
 
-
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-
 import java.io.File
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
@@ -23,11 +21,11 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
   var opt_adapter: Set[String] = Set()
-  if (configContains("adapter")) for (adapter <- config("adapter").getList) opt_adapter += adapter.toString
+  if (config.contains("adapter")) for (adapter <- config("adapter").getList) opt_adapter += adapter.toString
   var opt_anywhere: Set[String] = Set()
-  if (configContains("anywhere")) for (adapter <- config("anywhere").getList) opt_anywhere += adapter.toString
+  if (config.contains("anywhere")) for (adapter <- config("anywhere").getList) opt_anywhere += adapter.toString
   var opt_front: Set[String] = Set()
-  if (configContains("front")) for (adapter <- config("front").getList) opt_front += adapter.toString
+  if (config.contains("front")) for (adapter <- config("front").getList) opt_front += adapter.toString
 
   var opt_discard: Boolean = config("discard")
   var opt_minimum_length: String = config("minimum_length", 1)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -29,12 +29,12 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
     for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
-    if (configContains("targetBed")) {
+    if (config.contains("targetBed")) {
       for (file <- config("targetBed").getList) {
         bedFiles +:= new File(file.toString)
       }
     }
-    if (baitBedFile == null && configContains("targetBait")) baitBedFile = config("targetBait")
+    if (baitBedFile == null && config.contains("targetBait")) baitBedFile = config("targetBait")
   }
 
   def biopetScript() {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -25,7 +25,7 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
   var dbsnp: File = _
 
   def init() {
-    if (configContains("gvcffiles")) for (file <- config("gvcffiles").getList) {
+    if (config.contains("gvcffiles")) for (file <- config("gvcffiles").getList) {
       gvcfFiles ::= file.toString
     }
     if (reference == null) reference = config("reference")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -52,8 +52,8 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   def addGenotypeGVCFs(gvcfFiles: List[File], outputFile: File): File = {
     val genotypeGVCFs = new GenotypeGVCFs() with gatkArguments {
       this.variant = gvcfFiles
-      if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
-      if (configContains("scattercount", submodule = "genotypegvcfs"))
+      if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
+      if (config.contains("scattercount", submodule = "genotypegvcfs"))
         this.scatterCount = config("scattercount", submodule = "genotypegvcfs")
       this.out = outputFile
       if (config("inputtype", "dna").getString == "rna") {
@@ -73,7 +73,7 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
       this.variant = inputFile
       for (sample <- samples) this.sample_name :+= sample
       this.excludeNonVariants = true
-      if (configContains("scattercount", submodule = "selectvariants"))
+      if (config.contains("scattercount", submodule = "selectvariants"))
         this.scatterCount = config("scattercount", submodule = "selectvariants")
       this.out = outputDir + name + ".vcf"
     }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -31,7 +31,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     for (file <- configfiles) globalConfig.loadConfigFile(file)
     reference = config("reference", required = true)
     dbsnp = config("dbsnp")
-    if (configContains("gvcfFiles"))
+    if (config.contains("gvcfFiles"))
       for (file <- config("gvcfFiles").getList)
         gvcfFiles :+= file.toString
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
@@ -156,25 +156,25 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     val variantRecalibrator = new VariantRecalibrator() with gatkArguments {
       if (mode_arg == "indel") {
         this.mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
-        if (configContains("mills", submodule = "variantrecalibrator"))
+        if (config.contains("mills", submodule = "variantrecalibrator"))
           this.resource :+= new TaggedFile(config("mills", submodule = "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=12.0")
       } else { // SNP
         this.mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
-        if (configContains("hapmap", submodule = "variantrecalibrator"))
+        if (config.contains("hapmap", submodule = "variantrecalibrator"))
           this.resource +:= new TaggedFile(config("hapmap", submodule = "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=15.0")
-        if (configContains("omni", submodule = "variantrecalibrator"))
+        if (config.contains("omni", submodule = "variantrecalibrator"))
           this.resource +:= new TaggedFile(config("omni", submodule = "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=12.0")
-        if (configContains("1000G", submodule = "variantrecalibrator"))
+        if (config.contains("1000G", submodule = "variantrecalibrator"))
           this.resource +:= new TaggedFile(config("1000G", submodule = "variantrecalibrator").getString, "known=false,training=true,truth=false,prior=10.0")
       }
-      if (configContains("dbsnp", submodule = "variantrecalibrator"))
+      if (config.contains("dbsnp", submodule = "variantrecalibrator"))
         this.resource :+= new TaggedFile(config("dbsnp", submodule = "variantrecalibrator").getString, "known=true,training=false,truth=false,prior=2.0")
       this.nt = 4
       this.memoryLimit = nt * 2
       this.an = Seq("QD", "DP", "FS", "ReadPosRankSum", "MQRankSum")
-      if (configContains("minnumbadvariants", submodule = "variantrecalibrator"))
+      if (config.contains("minnumbadvariants", submodule = "variantrecalibrator"))
         this.minNumBadVariants = config("minnumbadvariants", submodule = "variantrecalibrator")
-      if (configContains("maxgaussians", submodule = "variantrecalibrator"))
+      if (config.contains("maxgaussians", submodule = "variantrecalibrator"))
         this.maxGaussians = config("maxgaussians", submodule = "variantrecalibrator")
     }
     return variantRecalibrator
@@ -191,7 +191,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       }
       this.nt = 3
       this.memoryLimit = nt * 2
-      if (configContains("scattercount", submodule = "applyrecalibration"))
+      if (config.contains("scattercount", submodule = "applyrecalibration"))
         this.scatterCount = config("scattercount", submodule = "applyrecalibration")
     }
     return applyRecalibration
@@ -203,7 +203,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       this.input_file = bamfiles
       this.dbsnp = config("dbsnp", submodule = "variantannotator")
       this.out = swapExt(dir, inputvcf, ".vcf", ".anotated.vcf")
-      if (configContains("scattercount", submodule = "variantannotator"))
+      if (config.contains("scattercount", submodule = "variantannotator"))
         this.scatterCount = config("scattercount", submodule = "variantannotator")
     }
     add(variantAnnotator)
@@ -215,7 +215,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     val combineGVCFs = new CombineGVCFs with gatkArguments {
       this.variant = input
       this.o = output
-      if (configContains("scattercount", submodule = "variantannotator"))
+      if (config.contains("scattercount", submodule = "variantannotator"))
         this.scatterCount = config("scattercount", submodule = "combinegvcfs")
     }
     add(combineGVCFs)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -63,7 +63,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       this.I :+= inputBam
       this.o = swapExt(dir, inputBam, ".bam", ".realign.intervals")
       this.jobResourceRequests :+= "h_vmem=5G"
-      if (configContains("scattercount", "realignertargetcreator")) this.scatterCount = config("scattercount", 1, "realignertargetcreator")
+      if (config.contains("scattercount", "realignertargetcreator")) this.scatterCount = config("scattercount", 1, "realignertargetcreator")
     }
     realignerTargetCreator.isIntermediate = true
     add(realignerTargetCreator)
@@ -72,7 +72,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       this.I :+= inputBam
       this.targetIntervals = realignerTargetCreator.o
       this.o = swapExt(dir, inputBam, ".bam", ".realign.bam")
-      if (configContains("scattercount", "indelrealigner")) this.scatterCount = config("scattercount", 1, "indelrealigner")
+      if (config.contains("scattercount", "indelrealigner")) this.scatterCount = config("scattercount", 1, "indelrealigner")
     }
     indelRealigner.isIntermediate = true
     add(indelRealigner)
@@ -85,7 +85,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       this.I :+= inputBam
       this.o = swapExt(dir, inputBam, ".bam", ".baserecal")
       if (dbsnp != null) this.knownSites :+= dbsnp
-      if (configContains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
+      if (config.contains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
       this.nct = config("threads", 1, "baserecalibrator")
     }
     add(baseRecalibrator)
@@ -95,7 +95,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       this.o = swapExt(dir, inputBam, ".bam", ".baserecal.after")
       this.BQSR = baseRecalibrator.o
       if (dbsnp != null) this.knownSites :+= dbsnp
-      if (configContains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
+      if (config.contains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
       this.nct = config("threads", 1, "baserecalibrator")
     }
     add(baseRecalibratorAfter)
@@ -111,7 +111,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       this.I :+= inputBam
       this.o = swapExt(dir, inputBam, ".bam", ".baserecal.bam")
       this.BQSR = baseRecalibrator.o
-      if (configContains("scattercount", "printreads")) this.scatterCount = config("scattercount", 1, "printreads")
+      if (config.contains("scattercount", "printreads")) this.scatterCount = config("scattercount", 1, "printreads")
     }
     printReads.isIntermediate = true
     add(printReads)
@@ -122,10 +122,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   def addHaplotypeCaller(bamfiles: List[File], outputfile: File): File = {
     val haplotypeCaller = new HaplotypeCaller with gatkArguments {
       this.min_mapping_quality_score = config("minMappingQualityScore", 20, "haplotypecaller")
-      if (configContains("scattercount", "haplotypecaller")) this.scatterCount = config("scattercount", 1, "haplotypecaller")
+      if (config.contains("scattercount", "haplotypecaller")) this.scatterCount = config("scattercount", 1, "haplotypecaller")
       this.input_file = bamfiles
       this.out = outputfile
-      if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
+      if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
       this.nct = config("threads", default = 3, submodule = "haplotypecaller")
       if (config("outputToBam", default = false, submodule = "haplotypecaller").getBoolean) {
         this.bamOutput = outputfile.getAbsolutePath + ".bam"
@@ -134,7 +134,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       }
       this.memoryLimit = this.nct * 2
       
-      if (configContains("allSitePLs")) this.allSitePLs = config("allSitePLs")
+      if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
       
       // GVCF options
       if (gvcfMode) {
@@ -165,8 +165,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
     val genotypeGVCFs = new GenotypeGVCFs() with gatkArguments {
       this.variant = gvcfFiles
       this.annotation ++= Seq("FisherStrand", "QualByDepth", "ChromosomeCounts")
-      if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
-      if (configContains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", 1, "genotypegvcfs")
+      if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
+      if (config.contains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", 1, "genotypegvcfs")
       this.out = outputDir + outputName + ".vcf"
       this.stand_call_conf = config("stand_call_conf", 30, "genotypegvcfs")
       this.stand_emit_conf = config("stand_emit_conf", 30, "genotypegvcfs")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala

@@ -33,7 +33,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   
   def init() {
     if (reference == null) reference = config("reference")
-    if (configContains("targetBed")) 
+    if (config.contains("targetBed")) 
       for (bed <- config("targetBed").getList) 
         targetBed :+= bed.toString
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -89,18 +89,18 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
     if (input_R1 == null) throw new IllegalStateException("Missing Fastq R1 on mapping module")
     paired = (input_R2 != null)
 
-    if (RGLB == null && configContains("RGLB")) RGLB = config("RGLB")
+    if (RGLB == null && config.contains("RGLB")) RGLB = config("RGLB")
     else if (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
-    if (RGSM == null && configContains("RGSM")) RGSM = config("RGSM")
+    if (RGSM == null && config.contains("RGSM")) RGSM = config("RGSM")
     else if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
-    if (RGID == null && configContains("RGID")) RGID = config("RGID")
+    if (RGID == null && config.contains("RGID")) RGID = config("RGID")
     else if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
     else if (RGID == null) throw new IllegalStateException("Missing Readgroup ID on mapping module")
 
     if (RGPL == null) RGPL = config("RGPL", "illumina")
     if (RGPU == null) RGPU = config("RGPU", "na")
-    if (RGCN == null && configContains("RGCN")) RGCN = config("RGCN")
-    if (RGDS == null && configContains("RGDS")) RGDS = config("RGDS")
+    if (RGCN == null && config.contains("RGCN")) RGCN = config("RGCN")
+    if (RGDS == null && config.contains("RGDS")) RGDS = config("RGDS")
 
     if (outputName == null) outputName = RGID
 
@@ -108,7 +108,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
     if (!chunking) chunking = config("chunking", false)
     if (chunking) {
       if (numberChunks.isEmpty) {
-        if (configContains("numberchunks")) numberChunks = config("numberchunks", default = None)
+        if (config.contains("numberchunks")) numberChunks = config("numberchunks", default = None)
         else {
           val chunkSize: Int = config("chunksize", (1 << 30))
           val filesize = if (input_R1.getName.endsWith(".gz") || input_R1.getName.endsWith(".gzip")) input_R1.length * 3