Allow users to turn off fix from 4.1.9.0 for consistency's sake

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 class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
     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 USER_DEFINED_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 +249,14 @@ public double getInitialLogOdds() {
     @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.
+     */
+    @Advanced
+    @Argument(fullName = USER_DEFINED_BASE_QUAL_CORRECTION, optional = true, doc = "Set to zero to turn off the error model changes included in GATK 4.1.9.0.")
+    public double userDefinedBaseQualCorrection = 1;
+
     /**
      * 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 @@ public final class Mutect2Engine implements AssemblyRegionEvaluator, AutoCloseab
 
     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 @@ public Mutect2Engine(final M2ArgumentCollection MTAC, AssemblyRegionArgumentColl
         aligner = SmithWatermanAligner.getAligner(MTAC.smithWatermanImplementation);
         samplesList = new IndexedSampleList(new ArrayList<>(ReadUtils.getSamplesFromHeader(header)));
 
+        tumorPileupQualBuffer = new PileupQualBuffer(MTAC.userDefinedBaseQualCorrection);
+        normalPileupQualBuffer = new PileupQualBuffer(MTAC.userDefinedBaseQualCorrection);
+
         // optimize set operations for the common cases of no normal and one normal
         if (MTAC.normalSamples.isEmpty()) {
             normalSamples = Collections.emptySet();
@@ -677,11 +680,17 @@ private static class PileupQualBuffer {
         // 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 USER_DEFINED_QUAL_CORRECTION = 1;
+
         // 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 userDefinedQualCorrection) {
+            USER_DEFINED_QUAL_CORRECTION = userDefinedQualCorrection;
+        }
+
         public void accumulateQuals(final ReadPileup pileup, final byte refBase, final int pcrErrorQual) {
             clear();
             final int position = pileup.getLocation().getStart();
@@ -731,7 +740,7 @@ private void accumulateSubstitution(final byte base, final byte qual) {
             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 + ONE_THIRD_QUAL_CORRECTION * USER_DEFINED_QUAL_CORRECTION, QualityUtils.MAX_QUAL));
             }
         }
 

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

@@ -119,8 +119,10 @@ public void testSmallNumAltExact(final int numRef, final double errorRate) {
 
             Assert.assertEquals(calculated, expected, precision);
         }
+    }
 
-
+    @Test
+    public void testOldErrorModelBehavior() {
 
     }