mutect2 expose param

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java

@@ -9,7 +9,6 @@
 import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection;
-import org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.*;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
 import org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls;
@@ -50,6 +49,7 @@
     public static final String CALLABLE_DEPTH_LONG_NAME = "callable-depth";
     public static final String PCR_SNV_QUAL_LONG_NAME = "pcr-snv-qual";
     public static final String PCR_INDEL_QUAL_LONG_NAME = "pcr-indel-qual";
+    public static final String MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION = "base-qual-correction-factor";
     public static final String F1R2_TAR_GZ_NAME = "f1r2-tar-gz";
 
     public static final double DEFAULT_AF_FOR_TUMOR_ONLY_CALLING = 5e-8;
@@ -249,6 +249,18 @@
     @Argument(fullName = PCR_INDEL_QUAL_LONG_NAME, optional = true, doc = "Phred-scaled PCR indel qual for overlapping fragments")
     public int pcrIndelQual = 40;
 
+    /**
+     * A scale factor to modify the base qualities reported by the sequencer and used in the Mutect2 substitution error model.
+     * Set to zero to turn off the error model changes included in GATK 4.1.9.0.
+     * Our pileup likelihoods models assume that the base quality (qual) corresponds to the probability that a ref base is misread
+     * as the *particular* alt base, whereas the qual actually means the probability of *any* substitution error.
+     * Since there are three possible substitutions for each ref base we must divide the error probability by three
+     * which corresponds to adding 10*log10(3) = 4.77 ~ 5 to the qual.
+     */
+    @Advanced
+    @Argument(fullName = MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION, optional = true, doc = "Set to zero to turn off the error model changes included in GATK 4.1.9.0.")
+    public int activeRegionMultipleSubstitutionBaseQualCorrection = (int)Math.round(10 * Math.log10(3));
+
     /**
      * In tumor-only mode, we discard variants with population allele frequencies greater than this threshold.
      */

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java

@@ -122,8 +122,8 @@
 
     private final Optional<F1R2CountsCollector> f1R2CountsCollector;
 
-    private PileupQualBuffer tumorPileupQualBuffer = new PileupQualBuffer();
-    private PileupQualBuffer normalPileupQualBuffer = new PileupQualBuffer();
+    private PileupQualBuffer tumorPileupQualBuffer;
+    private PileupQualBuffer normalPileupQualBuffer;
 
     /**
      * Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header,
@@ -144,6 +144,9 @@
         aligner = SmithWatermanAligner.getAligner(MTAC.smithWatermanImplementation);
         samplesList = new IndexedSampleList(new ArrayList<>(ReadUtils.getSamplesFromHeader(header)));
 
+        tumorPileupQualBuffer = new PileupQualBuffer(MTAC.activeRegionMultipleSubstitutionBaseQualCorrection);
+        normalPileupQualBuffer = new PileupQualBuffer(MTAC.activeRegionMultipleSubstitutionBaseQualCorrection);
+
         // optimize set operations for the common cases of no normal and one normal
         if (MTAC.normalSamples.isEmpty()) {
             normalSamples = Collections.emptySet();
@@ -671,16 +674,14 @@
         private static final int OTHER_SUBSTITUTION = 4;
         private static final int INDEL = 5;
 
-        // our pileup likelihoods models assume that the qual corresponds to the probability that a ref base is misread
-        // as the *particular* alt base, whereas the qual actually means the probability of *any* substitution error.
-        // since there are three possible substitutions for each ref base we must divide the error probability by three
-        // which corresponds to adding 10*log10(3) = 4.77 ~ 5 to the qual.
-        private static final int ONE_THIRD_QUAL_CORRECTION = 5;
+        private static double MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION;
 
         // indices 0-3 are A,C,G,T; 4 is other substitution (just in case it's some exotic protocol); 5 is indel
         private List<ByteArrayList> buffers = IntStream.range(0,6).mapToObj(n -> new ByteArrayList()).collect(Collectors.toList());
 
-        public PileupQualBuffer() { }
+        public PileupQualBuffer(final double multipleSubstitutionQualCorrection) {
+            MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION = multipleSubstitutionQualCorrection;
+        }
 
         public void accumulateQuals(final ReadPileup pileup, final byte refBase, final int pcrErrorQual) {
             clear();
@@ -731,7 +732,7 @@
             if (index == -1) {  // -1 is the hard-coded value for non-simple bases in BaseUtils
                 buffers.get(OTHER_SUBSTITUTION).add(qual);
             } else {
-                buffers.get(index).add((byte) FastMath.min(qual + ONE_THIRD_QUAL_CORRECTION, QualityUtils.MAX_QUAL));
+                buffers.get(index).add((byte) FastMath.min(qual + MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION, QualityUtils.MAX_QUAL));
             }
         }
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2EngineUnitTest.java

@@ -119,9 +119,6 @@ public void testSmallNumAltExact(final int numRef, final double errorRate) {
 
             Assert.assertEquals(calculated, expected, precision);
         }
-
-
-
     }
 
     @DataProvider(name = "fewAltData")