Renaming ContrastiveRecalibrator --> VariantRecalibrator in preparation for move to core

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5733 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java

@@ -123,7 +123,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
         // setup the header fields
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
-        hInfo.add(new VCFInfoHeaderLine(ContrastiveRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "log10-scaled probability of variant being true under the trained gaussian mixture model"));
+        hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "log10-scaled probability of variant being true under the trained gaussian mixture model"));
         final TreeSet<String> samples = new TreeSet<String>();
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
 
@@ -170,12 +170,12 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
 
         for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
             if( vc != null ) {
-                if( ContrastiveRecalibrator.checkRecalibrationMode( vc, MODE ) ) {
+                if( VariantRecalibrator.checkRecalibrationMode( vc, MODE ) ) {
                     String filterString = null;
                     final Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
                     final Double lod = (Double) lodMap.get( ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStop() );
                     if( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) {
-                        attrs.put(ContrastiveRecalibrator.VQS_LOD_KEY, String.format("%.4f", lod));
+                        attrs.put(VariantRecalibrator.VQS_LOD_KEY, String.format("%.4f", lod));
                         for( int i = tranches.size() - 1; i >= 0; i-- ) {
                             final Tranche tranche = tranches.get(i);
                             if( lod >= tranche.minVQSLod ) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java

@@ -48,15 +48,15 @@ import java.io.PrintStream;
 import java.util.*;
 
 /**
- * Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score.
+ * Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
  *
  * User: rpoplin
  * Date: 3/12/11
  *
- * @help.summary Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variants
+ * @help.summary Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
  */
 
-public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {
+public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {
 
     public static final String VQS_LOD_KEY = "VQSLOD";
 

scala/qscript/core/MethodsDevelopmentCallingPipeline.scala

@@ -244,7 +244,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
   }
 
   // 3.) Variant Quality Score Recalibration - Generate Recalibration table
-  class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator with UNIVERSAL_GATK_ARGS {
+  class VQSR(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
     this.memoryLimit = 4
     this.reference_sequence = t.reference
     this.intervalsString ++= List(t.intervals)

scala/qscript/oneoffs/carneiro/pbCalling.scala

@@ -187,7 +187,7 @@ class pbCalling extends QScript {
     this.analysisName = t.name + "_VF"
   }
 
-  class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator {
+  class VQSR(t: Target, goldStandard: Boolean) extends VariantRecalibrator {
     this.memoryLimit = 6
     this.intervalsString ++= List(t.intervals)
     this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )

scala/qscript/oneoffs/chartl/Exome_VQSR_FullSearch.q

@@ -154,7 +154,7 @@ class Exome_VQSR_FullSearch extends QScript {
         val directory = getPath(annotations,recalTogether)
         for ( call_thresh <- VQSR_CALL_THRESH ) {
           for ( vqsr_rb <- VQSR_RODBINDS.iterator ) {
-            trait VQSR_Args extends ContrastiveRecalibrator {
+            trait VQSR_Args extends VariantRecalibrator {
               this.allPoly = true
               this.analysisName = "VQSR_%s_%s_%.1f".format( annotations.reduceLeft( _ + "." + _), if ( recalTogether ) "true" else "false", call_thresh)
               this.commandDirectory = directory
@@ -166,17 +166,17 @@ class Exome_VQSR_FullSearch extends QScript {
             }
             val nameFormat = SCRIPT_BASE_NAME+".%1f.%s.".format(call_thresh,vqsr_rb._1)+"%s."
             if ( recalTogether ) {
-              var vqsr = new ContrastiveRecalibrator with VQSR_Args with ExpandedIntervals with CommandLineGATKArgs
+              var vqsr = new VariantRecalibrator with VQSR_Args with ExpandedIntervals with CommandLineGATKArgs
               vqsr.tranchesFile = new File(nameFormat.format("both")+"tranche")
               vqsr.recalFile = new File(nameFormat.format("both")+"recal")
               add(vqsr)
               addAll(eval(vqsr, ei.outList, "flanks"))
               addAll(eval(vqsr, INTS, "exons"))
             } else {
-              var exons = new ContrastiveRecalibrator with VQSR_Args with CommandLineGATKArgs
+              var exons = new VariantRecalibrator with VQSR_Args with CommandLineGATKArgs
               exons.tranchesFile = new File(nameFormat.format("exons")+"tranche")
               exons.recalFile = new File(nameFormat.format("exons")+"recal")
-              var flanks = new ContrastiveRecalibrator with VQSR_Args
+              var flanks = new VariantRecalibrator with VQSR_Args
               flanks.intervals :+= ei.outList.getAbsoluteFile
               flanks.jarFile = GATK_JAR
               flanks.memoryLimit = Some(8)
@@ -194,8 +194,8 @@ class Exome_VQSR_FullSearch extends QScript {
   }
 
   // want to apply and eval
-  def eval(recal: ContrastiveRecalibrator) : List[QFunction] = { eval(recal,null,"") }
+  def eval(recal: VariantRecalibrator) : List[QFunction] = { eval(recal,null,"") }
-  def eval(recal: ContrastiveRecalibrator, list: File, ext: String) : List[QFunction] = {
+  def eval(recal: VariantRecalibrator, list: File, ext: String) : List[QFunction] = {
     var functions : List[QFunction] = Nil
     trait ImplicitArgs extends CommandLineGATK {
       this.jarFile = recal.jarFile
@@ -245,4 +245,4 @@ class Exome_VQSR_FullSearch extends QScript {
 
     functions
   }
-}
+}

scala/qscript/playground/wgs.q

@@ -170,7 +170,7 @@ class WGSpipeline extends QScript {
     recombine.jobName = qscript.project + ".recombine"
     recombine.jobOutputFile = swapExt(combineVCFs.jobOutputFile, "combine.out", "recombine.out")
 
-    val cr = new ContrastiveRecalibrator with CommandLineGATKArgs
+    val cr = new VariantRecalibrator with CommandLineGATKArgs
       cr.rodBind :+= RodBind("hapmap","VCF",  qscript.hapmap,  "training=true, prior=3.0")
       cr.rodBind :+= RodBind("1kg", "VCF",  qscript.omni,  "training=true, prior=3.0")
       cr.rodBind :+= RodBind("input", "VCF", recombine.out)