Switch to beforeGraph

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -82,8 +82,8 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     deps ++= input.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     if (recal_file != null)
       deps :+= VcfUtils.getVcfIndexFile(recal_file)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -59,8 +59,8 @@ class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterG
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
     deps ++= variant.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -91,8 +91,8 @@ class CombineVariants(val root: Configurable) extends CommandLineGATK with Scatt
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     deps ++= variant.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
       if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(out.getPath))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -131,8 +131,8 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     deps ++= knownAlleles.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
       if (!disable_bam_indexing)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -62,8 +62,8 @@ class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGat
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
       if (!disable_bam_indexing)
         outputFiles :+= new File(out.getPath.stripSuffix(".bam") + ".bai")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -61,8 +61,8 @@ class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK wit
 
   if (config.contains("dbsnp")) known :+= new File(config("dbsnp").asString)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     deps ++= known.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
   }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -207,8 +207,8 @@ class SelectVariants(val root: Configurable) extends CommandLineGATK with Scatte
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     if (variant != null)
       deps :+= VcfUtils.getVcfIndexFile(variant)
     discordance.foreach(deps :+= VcfUtils.getVcfIndexFile(_))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -251,8 +251,8 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     reference_sample_calls.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
     alleles.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
     dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -8,36 +8,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import nl.lumc.sasc.biopet.utils.VcfUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
-
-//class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-//}
-//
-//object VariantEval {
-//  def apply(root: Configurable, sample: File, compareWith: File,
-//            output: File): VariantEval = {
-//    val vareval = new VariantEval(root)
-//    vareval.eval = Seq(sample)
-//    vareval.comp = Seq(compareWith)
-//    vareval.out = output
-//    vareval
-//  }
-//
-//  def apply(root: Configurable, sample: File, compareWith: File,
-//            output: File, ST: Seq[String], EV: Seq[String]): VariantEval = {
-//    val vareval = new VariantEval(root)
-//    vareval.eval = Seq(sample)
-//    vareval.comp = Seq(compareWith)
-//    vareval.out = output
-//    vareval.noST = true
-//    vareval.ST = ST
-//    vareval.noEV = true
-//    vareval.EV = EV
-//    vareval
-//  }
-//
-//}
-
 import java.io.File
 import org.broadinstitute.gatk.utils.commandline.Argument
 import org.broadinstitute.gatk.utils.commandline.Gather
@@ -160,8 +130,8 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     deps ++= eval.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -170,8 +170,8 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
+  override def beforeGraph() {
+    super.beforeGraph()
     deps ++= input.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     deps ++= aggregate.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     deps ++= resource.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))