Removing Beagle output from UG. Use ProduceBeagleInput walker instead (since it can be run post-filtration and respects the FILTER column).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3607 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java

@@ -104,7 +104,7 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
         }
 
         // update the engine
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, null, null, null);
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, null, null);
         UG_engine.samples = samples;        
 
         // initialize the header

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java

@@ -167,24 +167,6 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
             calls.put(sample, cg);
         }
 
-        // output to beagle file if requested
-        if ( beagleWriter != null ) {
-            for ( String sample : samples ) {
-                GenotypeLikelihoods gl = GLs.get(sample);
-                if ( gl == null ) {
-                    beagleWriter.print(" 0.0 0.0 0.0");
-                    continue;
-                }
-                double[] likelihoods = gl.getLikelihoods();
-                beagleWriter.print(' ');
-                beagleWriter.print(String.format("%.6f", Math.pow(10, likelihoods[refGenotype.ordinal()])));
-                beagleWriter.print(' ');
-                beagleWriter.print(String.format("%.6f", Math.pow(10, likelihoods[hetGenotype.ordinal()])));
-                beagleWriter.print(' ');
-                beagleWriter.print(String.format("%.6f", Math.pow(10, likelihoods[homGenotype.ordinal()])));
-            }
-        }
-
         return calls;
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java

@@ -31,7 +31,6 @@ public abstract class GenotypeCalculationModel implements Cloneable {
     protected Logger logger;
     protected GenotypeWriterFactory.GENOTYPE_FORMAT OUTPUT_FORMAT;
     protected PrintStream verboseWriter;
-    protected PrintStream beagleWriter;
 
     /**
      * Create a new GenotypeCalculationModel object
@@ -47,20 +46,17 @@ public abstract class GenotypeCalculationModel implements Cloneable {
      * @param UAC           unified arg collection
      * @param outputFormat  output format
      * @param verboseWriter verbose writer
-     * @param beagleWriter  beagle writer
      */
     protected void initialize(Set<String> samples,
                               Logger logger,
                               UnifiedArgumentCollection UAC,
                               GenotypeWriterFactory.GENOTYPE_FORMAT outputFormat,
-                              PrintStream verboseWriter,
+                              PrintStream verboseWriter) {
-                              PrintStream beagleWriter) {
         this.UAC = UAC.clone();
         this.samples = new TreeSet<String>(samples);
         OUTPUT_FORMAT = outputFormat;
         this.logger = logger;
         this.verboseWriter = verboseWriter;
-        this.beagleWriter = beagleWriter;
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java

@@ -52,7 +52,6 @@ public class GenotypeCalculationModelFactory {
      * @param UAC           the unified argument collection
      * @param outputFormat  the output format
      * @param verboseWriter verbose writer
-     * @param beagleWriter  beagle writer
      *
      * @return model
      */
@@ -60,8 +59,7 @@ public class GenotypeCalculationModelFactory {
                                                                    Logger logger,
                                                                    UnifiedArgumentCollection UAC,
                                                                    GenotypeWriterFactory.GENOTYPE_FORMAT outputFormat,
-                                                                   PrintStream verboseWriter,
+                                                                   PrintStream verboseWriter) {
-                                                                   PrintStream beagleWriter) {
         GenotypeCalculationModel gcm;
         switch ( UAC.genotypeModel ) {
             case JOINT_ESTIMATE:
@@ -78,7 +76,7 @@ public class GenotypeCalculationModelFactory {
             default: throw new RuntimeException("Unexpected GenotypeCalculationModel " + UAC.genotypeModel);
         }
 
-        gcm.initialize(samples, logger, UAC, outputFormat, verboseWriter, beagleWriter);
+        gcm.initialize(samples, logger, UAC, outputFormat, verboseWriter);
         return gcm;
     }
 }

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java

@@ -360,22 +360,9 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
         if ( !UAC.ALL_BASES_MODE && !passesEmitThreshold(phredScaledConfidence, bestAFguess) )
             return new VariantCallContext(passesCallThreshold(phredScaledConfidence));
 
-        // output to beagle file if requested
-        if ( beagleWriter != null ) {
-            beagleWriter.print(loc);
-            beagleWriter.print(' ');
-            beagleWriter.print((char)ref);
-            beagleWriter.print(' ');
-            beagleWriter.print((char)((byte)bestAlternateAllele));
-        }
-
         // populate the sample-specific data (output it to beagle also if requested)
         Map<String, Genotype> genotypes = makeGenotypeCalls(ref, bestAlternateAllele, bestAFguess, contexts, loc);
 
-        // close beagle record (if requested)
-        if ( beagleWriter != null )
-            beagleWriter.println();
-
         // next, the variant context data (alleles, attributes, etc.)
         ArrayList<Allele> alleles = new ArrayList<Allele>();
         alleles.add(Allele.create(ref, true));

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

@@ -9,8 +9,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 
 import java.util.*;
 
-import net.sf.samtools.util.SequenceUtil;
-
 public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
 
     private int MIN_COVERAGE = 6;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -57,9 +57,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     @Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
     public PrintStream verboseWriter = null;
 
-    @Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = false)
-    public PrintStream beagleWriter = null;
-
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
     protected String[] annotationsToUse = {};
 
@@ -106,7 +103,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     public void initialize() {
 
         annotationEngine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, verboseWriter, beagleWriter, annotationEngine);
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, verboseWriter, annotationEngine);
 
         // initialize the writers
         if ( verboseWriter != null ) {
@@ -117,12 +114,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
             }
             verboseWriter.println(header);
         }
-        if ( beagleWriter != null ) {
-            beagleWriter.print("marker alleleA alleleB");
-            for ( String sample : UG_engine.samples )
-                beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
-            beagleWriter.println();
-        }
 
         // initialize the header
         GenotypeWriterFactory.writeHeader(writer, GenomeAnalysisEngine.instance.getSAMFileHeader(), UG_engine.samples, getHeaderInfo());

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -75,27 +75,25 @@ public class UnifiedGenotyperEngine {
     protected Logger logger = null;
     protected GenotypeWriter genotypeWriter = null;
     protected PrintStream verboseWriter = null;
-    protected PrintStream beagleWriter = null;
 
     // samples in input
     protected Set<String> samples = new HashSet<String>();
 
 
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        initialize(toolkit, UAC, null, null, null, null, null);
+        initialize(toolkit, UAC, null, null, null, null);
     }
 
-    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, PrintStream beagleWriter, VariantAnnotatorEngine engine) {
+    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, VariantAnnotatorEngine engine) {
-        initialize(toolkit, UAC, logger, genotypeWriter, verboseWriter, beagleWriter, engine);
+        initialize(toolkit, UAC, logger, genotypeWriter, verboseWriter, engine);
 
     }
 
-    private void initialize(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, PrintStream beagleWriter, VariantAnnotatorEngine engine) {
+    private void initialize(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, VariantAnnotatorEngine engine) {
         this.UAC = UAC;
         this.logger = logger;
         this.genotypeWriter = genotypeWriter;
         this.verboseWriter = verboseWriter;
-        this.beagleWriter = beagleWriter;
         this.annotationEngine = engine;
 
         // deal with input errors
@@ -153,7 +151,7 @@ public class UnifiedGenotyperEngine {
                 else
                     throw new StingException("Unsupported genotype format: " + genotypeWriter.getClass().getName());
             }
-            gcm.set(GenotypeCalculationModelFactory.makeGenotypeCalculation(samples, logger, UAC, format, verboseWriter, beagleWriter));
+            gcm.set(GenotypeCalculationModelFactory.makeGenotypeCalculation(samples, logger, UAC, format, verboseWriter));
         }
 
         byte ref = refContext.getBase();
@@ -212,7 +210,7 @@ public class UnifiedGenotyperEngine {
             if ( stratifiedContexts == null )
                 return null;
 
-            DiploidGenotypePriors priors = new DiploidGenotypePriors((byte)ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_REFERENCE_ERROR);
+            DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_REFERENCE_ERROR);
             call = gcm.get().callLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts, priors);
 
             // annotate the call, if possible