LOD back to TLOD

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OriginalAlignment.java

@@ -15,7 +15,6 @@
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
 
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
@@ -44,9 +43,9 @@ public void annotate(ReferenceContext ref, VariantContext vc, Genotype g, Genoty
         Utils.nonNull(vc);
         Utils.nonNull(likelihoods);
 
-        final double[] lods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
+        final double[] lods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
         if (lods==null) {
-            warning.warn(String.format("One or more variant contexts is missing the 'LOD' annotation, %s will not be computed for these VariantContexts", GATKVCFConstants.ORIGINAL_CONTIG_MISMATCH_KEY));
+            warning.warn(String.format("One or more variant contexts is missing the 'TLOD' annotation, %s will not be computed for these VariantContexts", GATKVCFConstants.ORIGINAL_CONTIG_MISMATCH_KEY));
             return;
         }
         final int indexOfMaxLod = MathUtils.maxElementIndex(lods);

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/PolymorphicNuMT.java

@@ -18,7 +18,6 @@
 import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
 import org.spark_project.guava.collect.Range;
 
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
@@ -62,9 +61,9 @@ public void annotate(ReferenceContext ref, VariantContext vc, Genotype g, Genoty
         Utils.nonNull(gb);
         Utils.nonNull(vc);
         Utils.nonNull(likelihoods);
-        final double[] lods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
+        final double[] lods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
         if (lods==null) {
-            warning.warn(String.format("One or more variant contexts is missing the 'LOD' annotation, %s will not be computed for these VariantContexts", GATKVCFConstants.POTENTIAL_POLYMORPHIC_NUMT_KEY));
+            warning.warn(String.format("One or more variant contexts is missing the 'TLOD' annotation, %s will not be computed for these VariantContexts", GATKVCFConstants.POTENTIAL_POLYMORPHIC_NUMT_KEY));
             return;
         }
         final int indexOfMaxLod = MathUtils.maxElementIndex(lods);

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadOrientationArtifact.java

@@ -72,7 +72,7 @@ public void annotate(final ReferenceContext ref,
             return;
         }
 
-        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY, () -> null, -1);
+        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY, () -> null, -1);
         final int indexOfMaxTumorLod = MathUtils.maxElementIndex(tumorLods);
         final Allele altAllele = vc.getAlternateAllele(indexOfMaxTumorLod);
         final Nucleotide altBase = Nucleotide.valueOf(altAllele.toString());

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandArtifact.java

@@ -83,14 +83,14 @@ public void annotate(final ReferenceContext ref,
         pi.put(ART_REV, PRIOR_PROBABILITY_OF_ARTIFACT);
 
         // We use the allele with highest log odds score
-        final double[] lods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY, () -> null, -1);
+        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY, () -> null, -1);
 
-        if (lods==null) {
-            warning.warn("One or more variant contexts is missing the 'LOD' annotation, StrandArtifact will not be computed for these VariantContexts");
+        if (tumorLods==null) {
+            warning.warn("One or more variant contexts is missing the 'TLOD' annotation, StrandArtifact will not be computed for these VariantContexts");
             return;
         }
-        final int indexOfMaxLod = MathUtils.maxElementIndex(lods);
-        final Allele altAllele = vc.getAlternateAllele(indexOfMaxLod);
+        final int indexOfMaxTumorLod = MathUtils.maxElementIndex(tumorLods);
+        final Allele altAllele = vc.getAlternateAllele(indexOfMaxTumorLod);
 
         final Collection<ReadLikelihoods<Allele>.BestAllele> informativeBestAlleles = likelihoods.bestAllelesBreakingTies(g.getSampleName()).stream().
                 filter(ba -> ba.isInformative()).collect(Collectors.toList());

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

@@ -22,9 +22,9 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
     public static final String DEFAULT_AF_LONG_NAME = "af-of-alleles-not-in-resource";
     public static final String DEFAULT_AF_SHORT_NAME = "default-af";
     public static final String EMISSION_LOD_LONG_NAME = "tumor-lod-to-emit";
-    public static final String EMISSION_LOD_SHORT_NAME = "emit-lod";
-    public static final String INITIAL_LOD_LONG_NAME = "initial-tumor-lod";
-    public static final String INITIAL_LOD_SHORT_NAME = "init-lod";
+    public static final String EMISSION_TUMOR_LOD_SHORT_NAME = "emit-lod";
+    public static final String INITIAL_TUMOR_LOD_LONG_NAME = "initial-tumor-lod";
+    public static final String INITIAL_TUMOR_LOD_SHORT_NAME = "init-lod";
     public static final String INITIAL_PCR_ERROR_QUAL = "initial-pcr-qual";
     public static final String MAX_POPULATION_AF_LONG_NAME = "max-population-af";
     public static final String MAX_POPULATION_AF_SHORT_NAME = "max-af";
@@ -115,12 +115,12 @@ public double getDefaultAlleleFrequency() {
     public Boolean mitochondria = false;
 
     /**
-     * Only variants with LODs exceeding this threshold will be written to the VCF, regardless of filter status.
+     * Only variants with tumor LODs exceeding this threshold will be written to the VCF, regardless of filter status.
      * Set to less than or equal to tumor_lod. Increase argument value to reduce false positives in the callset.
      * Default setting of 3 is permissive and will emit some amount of negative training data that 
      * {@link FilterMutectCalls} should then filter.
      */
-    @Argument(fullName = EMISSION_LOD_LONG_NAME, shortName = EMISSION_LOD_SHORT_NAME, optional = true, doc = "LOD threshold to emit tumor variant to VCF.")
+    @Argument(fullName = EMISSION_LOD_LONG_NAME, shortName = EMISSION_TUMOR_LOD_SHORT_NAME, optional = true, doc = "LOD threshold to emit variant to VCF.")
     private double emissionLodArg = DEFAULT_EMISSION_LOD;
 
     public double getEmissionLod() {
@@ -130,7 +130,7 @@ public double getEmissionLod() {
     /**
      * Only variants with estimated tumor LODs exceeding this threshold will be considered active.
      */
-    @Argument(fullName = INITIAL_LOD_LONG_NAME, shortName = INITIAL_LOD_SHORT_NAME, optional = true, doc = "LOD threshold to consider pileup active.")
+    @Argument(fullName = INITIAL_TUMOR_LOD_LONG_NAME, shortName = INITIAL_TUMOR_LOD_SHORT_NAME, optional = true, doc = "LOD threshold to consider pileup active.")
     private double initialLod = DEFAULT_INITIAL_LOD;
 
     public double getInitialLod() {

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2FiltersArgumentCollection.java

@@ -8,7 +8,7 @@
 public class M2FiltersArgumentCollection extends AssemblyBasedCallerArgumentCollection {
     private static final long serialVersionUID = 9345L;
     public static final String LOG_SOMATIC_PRIOR_LONG_NAME = "log-somatic-prior";
-    public static final String LOD_LONG_NAME = "tumor-lod";
+    public static final String TUMOR_LOD_LONG_NAME = "tumor-lod";
     public static final String NORMAL_ARTIFACT_LOD_LONG_NAME = "normal-artifact-lod";
     public static final String NORMAL_P_VALUE_THRESHOLD_LONG_NAME = "normal-p-value-threshold";
     public static final String MAX_GERMLINE_POSTERIOR_LONG_NAME = "max-germline-posterior";
@@ -58,8 +58,8 @@ public class M2FiltersArgumentCollection extends AssemblyBasedCallerArgumentColl
     /**
      * Only variants with log odds ratios exceeding this threshold can pass filtering.
      */
-    @Argument(fullName = LOD_LONG_NAME, optional = true, doc = "LOD threshold for calling variant")
-    public double LOD_THRESHOLD = 5.3;
+    @Argument(fullName = TUMOR_LOD_LONG_NAME, optional = true, doc = "LOD threshold for calling variant")
+    public double TUMOR_LOD_THRESHOLD = 5.3;
 
     /**
      * This is a measure of the minimum evidence to support that a variant observed in the tumor is not also present in the normal

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2FilteringEngine.java

@@ -65,9 +65,9 @@ private void applyContaminationFilter(final M2FiltersArgumentCollection MTFAC, f
     }
 
     private void applyTriallelicFilter(final VariantContext vc, final FilterResult filterResult) {
-        if (vc.hasAttribute(GATKVCFConstants.LOD_KEY)) {
-            final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
-            final long numPassingAltAlleles = Arrays.stream(tumorLods).filter(x -> x > MTFAC.LOD_THRESHOLD).count();
+        if (vc.hasAttribute(GATKVCFConstants.TUMOR_LOD_KEY)) {
+            final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
+            final long numPassingAltAlleles = Arrays.stream(tumorLods).filter(x -> x > MTFAC.TUMOR_LOD_THRESHOLD).count();
 
             if (numPassingAltAlleles > MTFAC.numAltAllelesThreshold) {
                 filterResult.addFilter(GATKVCFConstants.MULTIALLELIC_FILTER_NAME);
@@ -109,7 +109,7 @@ private static void applyPanelOfNormalsFilter(final M2FiltersArgumentCollection
 
     private void applyBaseQualityFilter(final M2FiltersArgumentCollection MTFAC, final VariantContext vc, final FilterResult filterResult) {
         final int[] baseQualityByAllele = getIntArrayTumorField(vc, BaseQuality.KEY);
-        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
+        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
         final int indexOfMaxTumorLod = MathUtils.maxElementIndex(tumorLods);
 
         if (baseQualityByAllele != null && baseQualityByAllele[indexOfMaxTumorLod + 1] < MTFAC.minMedianBaseQuality) {
@@ -141,8 +141,8 @@ private void applyReadPositionFilter(final M2FiltersArgumentCollection MTFAC, fi
     }
 
     private void applyGermlineVariantFilter(final M2FiltersArgumentCollection MTFAC, final VariantContext vc, final FilterResult filterResult) {
-        if (vc.hasAttribute(GATKVCFConstants.LOD_KEY) && vc.hasAttribute(GATKVCFConstants.POPULATION_AF_VCF_ATTRIBUTE)) {
-            final double[] tumorLog10OddsIfSomatic = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
+        if (vc.hasAttribute(GATKVCFConstants.TUMOR_LOD_KEY) && vc.hasAttribute(GATKVCFConstants.POPULATION_AF_VCF_ATTRIBUTE)) {
+            final double[] tumorLog10OddsIfSomatic = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
             final Optional<double[]> normalLods = vc.hasAttribute(GATKVCFConstants.NORMAL_LOD_KEY) ?
                     Optional.of(GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.NORMAL_LOD_KEY)) : Optional.empty();
             final double[] populationAlleleFrequencies = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.POPULATION_AF_VCF_ATTRIBUTE);
@@ -188,11 +188,11 @@ private void applyGermlineVariantFilter(final M2FiltersArgumentCollection MTFAC,
     }
 
     private void applyInsufficientEvidenceFilter(final M2FiltersArgumentCollection MTFAC, final VariantContext vc, final FilterResult filterResult) {
-        if (vc.hasAttribute(GATKVCFConstants.LOD_KEY)) {
-            final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
+        if (vc.hasAttribute(GATKVCFConstants.TUMOR_LOD_KEY)) {
+            final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
 
-            if (MathUtils.arrayMax(tumorLods) < MTFAC.LOD_THRESHOLD) {
-                filterResult.addFilter(GATKVCFConstants.LOW_LOD_FILTER_NAME);
+            if (MathUtils.arrayMax(tumorLods) < MTFAC.TUMOR_LOD_THRESHOLD) {
+                filterResult.addFilter(GATKVCFConstants.TUMOR_LOD_FILTER_NAME);
             }
         }
     }
@@ -201,11 +201,11 @@ private void applyInsufficientEvidenceFilter(final M2FiltersArgumentCollection M
     // this handles shared artifacts, such as ones due to alignment and any shared aspects of sequencing
     private void applyArtifactInNormalFilter(final M2FiltersArgumentCollection MTFAC, final VariantContext vc, final FilterResult filterResult) {
         if (!( vc.hasAttribute(GATKVCFConstants.NORMAL_ARTIFACT_LOD_ATTRIBUTE)
-                && vc.hasAttribute(GATKVCFConstants.LOD_KEY))) {
+                && vc.hasAttribute(GATKVCFConstants.TUMOR_LOD_KEY))) {
             return;
         }
 
-        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.LOD_KEY);
+        final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY);
         final int indexOfMaxTumorLod = MathUtils.maxElementIndex(tumorLods);
 
         Genotype tumorGenotype = vc.getGenotype(tumorSample);
@@ -339,7 +339,7 @@ private void applyChimericOriginalAlignmentFilter(final M2FiltersArgumentCollect
     }
     private void applyLODFilter(final M2FiltersArgumentCollection MTFAC, final VariantContext vc, final FilterResult filterResult) {
         if(vc.isBiallelic()) {
-            final Double lod = vc.getAttributeAsDouble(GATKVCFConstants.LOD_KEY, 1);
+            final Double lod = vc.getAttributeAsDouble(GATKVCFConstants.TUMOR_LOD_KEY, 1);
             final Double depth = vc.getAttributeAsDouble(VCFConstants.DEPTH_KEY, 1);
             final Double lodByDepth = lod / depth;
             if (lodByDepth < MTFAC.lodByDepth) {

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

@@ -11,7 +11,6 @@
 import org.apache.commons.math3.util.FastMath;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
-import org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculator;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculatorProvider;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerGenotypingEngine;
@@ -151,7 +150,7 @@ public CalledHaplotypes callMutations(
             final VariantContextBuilder callVcb = new VariantContextBuilder(mergedVC)
                     .alleles(allAllelesToEmit)
                     .attributes(populationAFAnnotation)
-                    .attribute(GATKVCFConstants.LOD_KEY, tumorAltAlleles.stream().mapToDouble(tumorLog10Odds::getAlt).toArray());
+                    .attribute(GATKVCFConstants.TUMOR_LOD_KEY, tumorAltAlleles.stream().mapToDouble(tumorLog10Odds::getAlt).toArray());
 
             normalLog10Odds.ifPresent(values -> callVcb.attribute(GATKVCFConstants.NORMAL_LOD_KEY, values.asDoubleArray(tumorAltAlleles)));
             normalArtifactLog10Odds.ifPresent(values -> callVcb.attribute(GATKVCFConstants.NORMAL_ARTIFACT_LOD_ATTRIBUTE, values.asDoubleArray(tumorAltAlleles)));

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java

@@ -2,7 +2,6 @@
 
 import htsjdk.variant.variantcontext.Allele;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
@@ -105,14 +104,14 @@ public final class GATKVCFConstants {
     public static final String F2R1_KEY =                           "F2R1";
 
     // Mutect2-specific INFO keys
-    public static final String LOD_KEY =                            "LOD";
+    public static final String TUMOR_LOD_KEY =                      "TLOD";
     public static final String NORMAL_LOD_KEY =                     "NLOD";
     public static final String IN_PON_VCF_ATTRIBUTE =               "IN_PON";
     public static final String NORMAL_ARTIFACT_LOD_ATTRIBUTE =      "N_ART_LOD";
     public static final String POPULATION_AF_VCF_ATTRIBUTE =        "POP_AF";
     public static final String GERMLINE_POSTERIORS_VCF_ATTRIBUTE =  "P_GERMLINE";
     public static final String POSTERIOR_PROB_OF_CONTAMINATION_ATTRIBUTE =  "P_CONTAM";
-    public static final List<String> STANDARD_MUTECT_INFO_FIELDS = Arrays.asList(NORMAL_LOD_KEY, LOD_KEY, NORMAL_ARTIFACT_LOD_ATTRIBUTE,
+    public static final List<String> STANDARD_MUTECT_INFO_FIELDS = Arrays.asList(NORMAL_LOD_KEY, TUMOR_LOD_KEY, NORMAL_ARTIFACT_LOD_ATTRIBUTE,
             EVENT_COUNT_IN_HAPLOTYPE_KEY, IN_PON_VCF_ATTRIBUTE, POPULATION_AF_VCF_ATTRIBUTE, GERMLINE_POSTERIORS_VCF_ATTRIBUTE, POSTERIOR_PROB_OF_CONTAMINATION_ATTRIBUTE);
 
     // FORMAT keys
@@ -154,7 +153,7 @@ their names (or descriptions) depend on some threshold.  Those filters are not i
     public static final String ALIGNMENT_ARTIFACT_FILTER_NAME =               "alignment_artifact";
     public static final String PON_FILTER_NAME =                              "panel_of_normals"; //M2
     public static final String STR_CONTRACTION_FILTER_NAME =                  "str_contraction"; //M2
-    public final static String LOW_LOD_FILTER_NAME =                          "low_lod"; //M2
+    public final static String TUMOR_LOD_FILTER_NAME =                        "t_lod"; //M2
     public static final String MULTIALLELIC_FILTER_NAME =                     "multiallelic"; //M2
     public static final String STRAND_ARTIFACT_FILTER_NAME =                  "strand_artifact"; // M2
     public static final String DUPLICATED_EVIDENCE_FILTER_NAME =              "duplicate_evidence";
@@ -171,7 +170,7 @@ their names (or descriptions) depend on some threshold.  Those filters are not i
 
 
     public static final List<String> MUTECT_FILTER_NAMES = Arrays.asList(STR_CONTRACTION_FILTER_NAME,
-            PON_FILTER_NAME, CLUSTERED_EVENTS_FILTER_NAME, LOW_LOD_FILTER_NAME, GERMLINE_RISK_FILTER_NAME,
+            PON_FILTER_NAME, CLUSTERED_EVENTS_FILTER_NAME, TUMOR_LOD_FILTER_NAME, GERMLINE_RISK_FILTER_NAME,
             MULTIALLELIC_FILTER_NAME, STRAND_ARTIFACT_FILTER_NAME, ARTIFACT_IN_NORMAL_FILTER_NAME,
             MEDIAN_BASE_QUALITY_FILTER_NAME, MEDIAN_MAPPING_QUALITY_FILTER_NAME,
             MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME,