Refactor ExactCallLogger into a separate class

-- Update minor integration tests with NanoSchedule due to qual accuracy update

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java

@@ -18,11 +18,8 @@ import java.io.*;
 import java.util.*;
 
 /**
- * Created with IntelliJ IDEA.
+ * A simple GATK utility (i.e, runs from command-line) for assessing the performance of
- * User: depristo
+ * the exact model
- * Date: 10/2/12
- * Time: 10:25 AM
- * To change this template use File | Settings | File Templates.
  */
 public class AFCalcPerformanceTest {
     final static Logger logger = Logger.getLogger(AFCalcPerformanceTest.class);
@@ -222,9 +219,9 @@ public class AFCalcPerformanceTest {
         final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(ref);
         final GenomeLocParser parser = new GenomeLocParser(seq);
         final BufferedReader reader = new BufferedReader(new FileReader(exactLogFile));
-        final List<AFCalc.ExactCall> loggedCalls = AFCalc.readExactLog(reader, startsToUse, parser);
+        final List<ExactCallLogger.ExactCall> loggedCalls = ExactCallLogger.readExactLog(reader, startsToUse, parser);
 
-        for ( final AFCalc.ExactCall call : loggedCalls ) {
+        for ( final ExactCallLogger.ExactCall call : loggedCalls ) {
             final AFCalcTestBuilder testBuilder = new AFCalcTestBuilder(call.vc.getNSamples(), 1,
                     AFCalcFactory.Calculation.EXACT_INDEPENDENT,
                     AFCalcTestBuilder.PriorType.human);

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java

@@ -28,20 +28,17 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.SimpleTimer;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.*;
+import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedList;
 import java.util.List;
 
 
 /**
  * Generic interface for calculating the probability of alleles segregating given priors and genotype likelihoods
- *
  */
 public abstract class AFCalc implements Cloneable {
     private final static Logger defaultLogger = Logger.getLogger(AFCalc.class);
@@ -53,8 +50,8 @@ public abstract class AFCalc implements Cloneable {
     protected Logger logger = defaultLogger;
 
     private SimpleTimer callTimer = new SimpleTimer();
-    private PrintStream callReport = null;
     private final AFCalcResultTracker resultTracker;
+    private ExactCallLogger exactCallLogger = null;
 
     protected AFCalc(final int nSamples, final int maxAltAlleles, final int maxAltAllelesForIndels, final int ploidy) {
         if ( nSamples < 0 ) throw new IllegalArgumentException("nSamples must be greater than zero " + nSamples);
@@ -69,7 +66,7 @@ public abstract class AFCalc implements Cloneable {
     }
 
     public void enableProcessLog(final File exactCallsLog) {
-        initializeOutputFile(exactCallsLog);
+        exactCallLogger = new ExactCallLogger(exactCallsLog);
     }
 
     public void setLogger(Logger logger) {
@@ -97,8 +94,8 @@ public abstract class AFCalc implements Cloneable {
         final AFCalcResult result = computeLog10PNonRef(vcWorking, log10AlleleFrequencyPriors);
         final long nanoTime = callTimer.getElapsedTimeNano();
 
-        if ( callReport != null )
+        if ( exactCallLogger != null )
-            printCallInfo(vcWorking, log10AlleleFrequencyPriors, nanoTime, resultTracker.getLog10PosteriorOfAFzero());
+            exactCallLogger.printCallInfo(vcWorking, log10AlleleFrequencyPriors, nanoTime, result);
 
         return result;
     }
@@ -165,130 +162,6 @@ public abstract class AFCalc implements Cloneable {
         return Math.max(maxAlternateAllelesToGenotype, maxAlternateAllelesForIndels);
     }
 
-
-    // ---------------------------------------------------------------------------
-    //
-    // Print information about the call to the calls log
-    //
-    // ---------------------------------------------------------------------------
-
-    private 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);
-        }
-    }
-
-    private void printCallInfo(final VariantContext vc,
-                               final double[] log10AlleleFrequencyPriors,
-                               final long runtimeNano,
-                               final double log10PosteriorOfAFzero) {
-        printCallElement(vc, "type", "ignore", vc.getType());
-
-        int allelei = 0;
-        for ( final Allele a : vc.getAlleles() )
-            printCallElement(vc, "allele", allelei++, a.getDisplayString());
-
-        for ( final Genotype g : vc.getGenotypes() )
-            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)));
-    }
-
-    public static class ExactCall {
-        final VariantContext vc;
-        final long origNanoTime;
-        long newNanoTime = -1;
-        final double origPNonRef;
-        double newPNonRef = -1;
-
-        public ExactCall(VariantContext vc, long origNanoTime, double origPNonRef) {
-            this.vc = vc;
-            this.origNanoTime = origNanoTime;
-            this.origPNonRef = origPNonRef;
-        }
-
-        @Override
-        public String toString() {
-            return String.format("ExactCall %s:%d alleles=%s nSamples=%s orig.pNonRef=%.2f orig.runtime=%s new.pNonRef=%.2f new.runtime=%s",
-                    vc.getChr(), vc.getStart(), vc.getAlleles(), vc.getNSamples(),
-                    origPNonRef,
-                    new AutoFormattingTime(origNanoTime / 1e9).toString(),
-                    newPNonRef,
-                    newNanoTime == -1 ? "not.run" : new AutoFormattingTime(newNanoTime / 1e9).toString());
-        }
-    }
-
-    public static List<ExactCall> readExactLog(final BufferedReader reader, final List<Integer> startsToKeep, GenomeLocParser parser) throws IOException {
-        List<ExactCall> calls = new LinkedList<ExactCall>();
-
-        // skip the header line
-        reader.readLine();
-
-        while ( true ) {
-            final VariantContextBuilder builder = new VariantContextBuilder();
-            final List<Allele> alleles = new ArrayList<Allele>();
-            final List<Genotype> genotypes = new ArrayList<Genotype>();
-            long runtimeNano = -1;
-
-            GenomeLoc currentLoc = null;
-            while ( true ) {
-                final String line = reader.readLine();
-                if ( line == null )
-                    return calls;
-
-                final String[] parts = line.split("\t");
-                final GenomeLoc lineLoc = parser.parseGenomeLoc(parts[0]);
-                final String variable = parts[1];
-                final String key = parts[2];
-                final String value = parts[3];
-
-                if ( currentLoc == null )
-                    currentLoc = lineLoc;
-
-                if ( variable.equals("log10PosteriorOfAFzero") ) {
-                    if ( startsToKeep.isEmpty() || startsToKeep.contains(currentLoc.getStart()) ) {
-                        builder.alleles(alleles);
-                        final int stop = currentLoc.getStart() + alleles.get(0).length() - 1;
-                        builder.chr(currentLoc.getContig()).start(currentLoc.getStart()).stop(stop);
-                        builder.genotypes(genotypes);
-                        calls.add(new ExactCall(builder.make(), runtimeNano, Double.valueOf(value)));
-                    }
-                    break;
-                } else if ( variable.equals("allele") ) {
-                    final boolean isRef = key.equals("0");
-                    alleles.add(Allele.create(value, isRef));
-                } else if ( variable.equals("PL") ) {
-                    final GenotypeBuilder gb = new GenotypeBuilder(key);
-                    gb.PL(GenotypeLikelihoods.fromPLField(value).getAsPLs());
-                    genotypes.add(gb.make());
-                } else if ( variable.equals("runtime.nano") ) {
-                    runtimeNano = Long.valueOf(value);
-                } else {
-                    // nothing to do
-                }
-            }
-        }
-    }
-
     public AFCalcResultTracker getResultTracker() {
         return resultTracker;
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java

@@ -0,0 +1,166 @@
+package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
+
+import org.broadinstitute.sting.utils.AutoFormattingTime;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.*;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+
+/**
+ * Allows us to write out and read in information about exact calls (site, alleles, PLs, etc) in tabular format
+ */
+public class ExactCallLogger implements Cloneable {
+    private PrintStream callReport = null;
+
+    /**
+     * Create a new ExactCallLogger writing it's output to outputFile
+     *
+     * @param outputFile
+     */
+    public ExactCallLogger(final File outputFile) {
+        try {
+            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);
+        }
+    }
+
+    /**
+     * Summarizes information about an exact call that happened
+     */
+    public static class ExactCall {
+        final VariantContext vc;
+        final long origNanoTime;
+        long newNanoTime = -1;
+        final double origPNonRef;
+        double newPNonRef = -1;
+
+        public ExactCall(VariantContext vc, long origNanoTime, double origPNonRef) {
+            this.vc = vc;
+            this.origNanoTime = origNanoTime;
+            this.origPNonRef = origPNonRef;
+        }
+
+        @Override
+        public String toString() {
+            return String.format("ExactCall %s:%d alleles=%s nSamples=%s orig.pNonRef=%.2f orig.runtime=%s new.pNonRef=%.2f new.runtime=%s",
+                    vc.getChr(), vc.getStart(), vc.getAlleles(), vc.getNSamples(),
+                    origPNonRef,
+                    new AutoFormattingTime(origNanoTime / 1e9).toString(),
+                    newPNonRef,
+                    newNanoTime == -1 ? "not.run" : new AutoFormattingTime(newNanoTime / 1e9).toString());
+        }
+    }
+
+    protected void printCallInfo(final VariantContext vc,
+                                 final double[] log10AlleleFrequencyPriors,
+                                 final long runtimeNano,
+                                 final AFCalcResult result) {
+        printCallElement(vc, "type", "ignore", vc.getType());
+
+        int allelei = 0;
+        for (final Allele a : vc.getAlleles())
+            printCallElement(vc, "allele", allelei++, a.getDisplayString());
+
+        for (final Genotype g : vc.getGenotypes())
+            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, "log10PosteriorOfAFEq0", "ignore", result.getLog10PosteriorOfAFEq0());
+        printCallElement(vc, "log10PosteriorOfAFGt0", "ignore", result.getLog10PosteriorOfAFGT0());
+
+        for ( final Allele allele : result.getAllelesUsedInGenotyping() ) {
+            if ( allele.isNonReference() ) {
+                printCallElement(vc, "MLE", allele, result.getAlleleCountAtMLE(allele));
+                printCallElement(vc, "pNonRefByAllele", allele, result.getLog10PosteriorOfAFGt0ForAllele(allele));
+            }
+        }
+
+        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)));
+    }
+
+    /**
+     * Read in a list of ExactCall objects from reader, keeping only those
+     * with starts in startsToKeep or all sites (if this is empty)
+     *
+     * @param reader
+     * @param startsToKeep
+     * @param parser
+     * @return
+     * @throws IOException
+     */
+    public static List<ExactCall> readExactLog(final BufferedReader reader, final List<Integer> startsToKeep, GenomeLocParser parser) throws IOException {
+        if ( reader == null ) throw new IllegalArgumentException("reader cannot be null");
+        if ( startsToKeep == null ) throw new IllegalArgumentException("startsToKeep cannot be null");
+        if ( parser == null ) throw new IllegalArgumentException("GenomeLocParser cannot be null");
+
+        List<ExactCall> calls = new LinkedList<ExactCall>();
+
+        // skip the header line
+        reader.readLine();
+
+        while (true) {
+            final VariantContextBuilder builder = new VariantContextBuilder();
+            final List<Allele> alleles = new ArrayList<Allele>();
+            final List<Genotype> genotypes = new ArrayList<Genotype>();
+            long runtimeNano = -1;
+
+            GenomeLoc currentLoc = null;
+            while (true) {
+                final String line = reader.readLine();
+                if (line == null)
+                    return calls;
+
+                final String[] parts = line.split("\t");
+                final GenomeLoc lineLoc = parser.parseGenomeLoc(parts[0]);
+                final String variable = parts[1];
+                final String key = parts[2];
+                final String value = parts[3];
+
+                if (currentLoc == null)
+                    currentLoc = lineLoc;
+
+                if (variable.equals("log10PosteriorOfAFzero")) {
+                    if (startsToKeep.isEmpty() || startsToKeep.contains(currentLoc.getStart())) {
+                        builder.alleles(alleles);
+                        final int stop = currentLoc.getStart() + alleles.get(0).length() - 1;
+                        builder.chr(currentLoc.getContig()).start(currentLoc.getStart()).stop(stop);
+                        builder.genotypes(genotypes);
+                        calls.add(new ExactCall(builder.make(), runtimeNano, Double.valueOf(value)));
+                    }
+                    break;
+                } else if (variable.equals("allele")) {
+                    final boolean isRef = key.equals("0");
+                    alleles.add(Allele.create(value, isRef));
+                } else if (variable.equals("PL")) {
+                    final GenotypeBuilder gb = new GenotypeBuilder(key);
+                    gb.PL(GenotypeLikelihoods.fromPLField(value).getAsPLs());
+                    genotypes.add(gb.make());
+                } else if (variable.equals("runtime.nano")) {
+                    runtimeNano = Long.valueOf(value);
+                } else {
+                    // nothing to do
+                }
+            }
+        }
+    }
+}

public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java

@@ -21,7 +21,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
             for ( final int nct : Arrays.asList(1, 2) ) {
 //                tests.add(new Object[]{ "SNP",   "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct });
 ////                tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
-                tests.add(new Object[]{ "BOTH",  "f8184e336dec7632408aa9afa98e6914", nt, nct });
+                tests.add(new Object[]{ "BOTH",  "8cad82c3a5f5b932042933f136663c8a", nt, nct });
             }
 
         return tests.toArray(new Object[][]{});