Add exactCallsLog output file to ExactModel and StandardCallerArgumentCollection

-- This allows us to log all of the information about the exact model call (alleles, priors, PLs, result, and runtime) to a file for later debugging / optimization

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java

@@ -237,9 +237,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC.clone(), logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
         UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling
         UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling
-        UAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING);
+        UAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING );
-        UAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING);
+        UAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING );
-        UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
+
+        // create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
+        UnifiedArgumentCollection simpleUAC = UAC.clone();
+        simpleUAC.exactCallsLog = null;
+        UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
 
         // initialize the output VCF header
         annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());

public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java

@@ -1,13 +1,12 @@
 package org.broadinstitute.sting.gatk.arguments;
 
-import org.broadinstitute.sting.commandline.Advanced;
+import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.io.File;
+
 /**
  * Created with IntelliJ IDEA.
  * User: rpoplin
@@ -59,4 +58,8 @@ public class StandardCallerArgumentCollection {
     @Advanced
     @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
     public int MAX_ALTERNATE_ALLELES = 3;
+
+    @Hidden
+    @Argument(shortName = "logExactCalls", doc="x")
+    public File exactCallsLog = null;
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java

@@ -27,12 +27,20 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.SimpleTimer;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.PrintStream;
 import java.util.*;
 
 public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
+    private SimpleTimer callTimer = new SimpleTimer();
+    private PrintStream callReport = null;
 
     // private final static boolean DEBUG = false;
 
@@ -40,6 +48,19 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
     protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {
         super(UAC, N, logger, verboseWriter);
+        if ( UAC.exactCallsLog != null )
+            initializeOutputFile(UAC.exactCallsLog);
+    }
+
+    public void initializeOutputFile(final File outputFile) {
+        try {
+            if (outputFile != null) {
+                callReport = new PrintStream( new FileOutputStream(outputFile) );
+                callReport.println(Utils.join("\t", Arrays.asList("loc", "variable", "key", "value")));
+            }
+        } catch ( FileNotFoundException e ) {
+            throw new UserException.CouldNotCreateOutputFile(outputFile, e);
+        }
     }
 
     public List<Allele> getLog10PNonRef(final VariantContext vc,
@@ -61,11 +82,44 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
             GLs = VariantContextUtils.subsetDiploidAlleles(vc, alleles, false);
         }
 
+        callTimer.start();
         linearExactMultiAllelic(GLs, alleles.size() - 1, log10AlleleFrequencyPriors, result);
+        final long nanoTime = callTimer.getElapsedTimeNano();
+
+        if ( callReport != null )
+            printCallInfo(vc, alleles, GLs, log10AlleleFrequencyPriors, nanoTime, result.getLog10PosteriorOfAFzero());
 
         return alleles;
     }
 
+    private void printCallInfo(final VariantContext vc,
+                               final List<Allele> alleles,
+                               final GenotypesContext GLs,
+                               final double[] log10AlleleFrequencyPriors,
+                               final long runtimeNano,
+                               final double log10PosteriorOfAFzero) {
+        printCallElement(vc, "type", "ignore", vc.getType());
+
+        int allelei = 0;
+        for ( final Allele a : alleles )
+            printCallElement(vc, "allele", allelei++, a.getDisplayString());
+
+        for ( final Genotype g : GLs )
+            printCallElement(vc, "PL", g.getSampleName(), g.getLikelihoodsString());
+
+        for ( int priorI = 0; priorI < log10AlleleFrequencyPriors.length; priorI++ )
+            printCallElement(vc, "priorI", priorI, log10AlleleFrequencyPriors[priorI]);
+
+        printCallElement(vc, "runtime.nano", "ignore", runtimeNano);
+        printCallElement(vc, "log10PosteriorOfAFzero", "ignore", log10PosteriorOfAFzero);
+
+        callReport.flush();
+    }
+
+    private void printCallElement(final VariantContext vc, final Object variable, final Object key, final Object value) {
+        final String loc = String.format("%s:%d", vc.getChr(), vc.getStart());
+        callReport.println(Utils.join("\t", Arrays.asList(loc, variable, key, value)));
+    }
 
     private static final int PL_INDEX_OF_HOM_REF = 0;
     private static List<Allele> chooseMostLikelyAlternateAlleles(VariantContext vc, int numAllelesToChoose) {

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -186,7 +186,6 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
     @Argument(shortName="ef", fullName="exclude_filtered_reference_sites", doc="Don't include in the analysis sites where the reference sample VCF is filtered. Default: false.", required=false)
     boolean EXCLUDE_FILTERED_REFERENCE_SITES = false;
 
-
     // Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
     public UnifiedArgumentCollection clone() {
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
@@ -224,6 +223,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
         uac.minReferenceDepth = minReferenceDepth;
         uac.EXCLUDE_FILTERED_REFERENCE_SITES = EXCLUDE_FILTERED_REFERENCE_SITES;
         uac.IGNORE_LANE_INFO = IGNORE_LANE_INFO;
+        uac.exactCallsLog = exactCallsLog;
 
         // todo- arguments to remove
         uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;
@@ -242,5 +242,6 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
         this.OutputMode = SCAC.OutputMode;
         this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
         this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
+        this.exactCallsLog = SCAC.exactCallsLog;
     }
 }