cnn variant update models validate scores cleanup training

build.gradle

@@ -63,7 +63,7 @@ final barclayVersion = System.getProperty('barclay.version','2.1.0')
 final sparkVersion = System.getProperty('spark.version', '2.2.0')
 final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
 final hadoopBamVersion = System.getProperty('hadoopBam.version','7.10.0')
-final tensorflowVersion = System.getProperty('tensorflow.version','1.4.0')
+final tensorflowVersion = System.getProperty('tensorflow.version','1.9.0')
 final genomicsdbVersion = System.getProperty('genomicsdb.version','0.10.0-proto-3.0.0-beta-1+bdce8be25b873')
 final testNGVersion = '6.11'
 // Using the shaded version to avoid conflicts between its protobuf dependency

scripts/gatkcondaenv.yml.template

@@ -26,7 +26,7 @@ dependencies:
   - h5py==2.7.1
   - html5lib==0.9999999
   - joblib==0.11
-  - keras==2.1.4
+  - keras==2.2.0
   - markdown==2.6.9
   - matplotlib==2.1.0
   - numpy==1.13.3
@@ -44,8 +44,7 @@ dependencies:
   - scipy==1.0.0
   - six==1.11.0
   - $tensorFlowDependency
-  - tensorflow-tensorboard==0.4.0rc3
   - theano==0.9.0
   - tqdm==4.19.4
   - werkzeug==0.12.2
-  - gatkPythonPackageArchive.zip
+  - gatkPythonPackageArchive.zip

src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/EvaluateInfoFieldConcordance.java

@@ -0,0 +1,191 @@
+package org.broadinstitute.hellbender.tools.walkers.validation;
+
+import java.nio.file.Paths;
+import java.io.IOException;
+
+import org.apache.commons.collections4.Predicate;
+
+import htsjdk.variant.variantcontext.VariantContext;
+
+import org.broadinstitute.barclay.argparser.Advanced;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.BetaFeature;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+
+import org.broadinstitute.hellbender.engine.ReadsContext;
+import org.broadinstitute.hellbender.engine.ReferenceContext;
+import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.engine.AbstractConcordanceWalker;
+
+import picard.cmdline.programgroups.VariantEvaluationProgramGroup;
+
+/**
+ * Compare INFO field values between two VCFs or compare two different INFO fields from one VCF.
+ * We only evaluate sites that are in both VCFs.
+ * Although we use the arguments eval and truth, we only compare the scores, we do not determine the correct score.
+ * Either VCF can be used as eval or truth, or the same VCF can be used for both.
+ * Differences greater than the epsilon argument will trigger a warning.
+ *
+ * <h3>Compare the CNN_2D info fields for the same sites from two different VCFs:</h3>
+ *
+ * <pre>
+ * gatk EvaluateInfoFieldConcordance \
+ *  -eval a.vcf \
+ *  -truth another.vcf \
+ *  -S summary.txt \
+ *  -eval-info-key CNN_2D \
+ *  -truth-info-key CNN_2D \
+ *  -epsilon 0.01
+ * </pre>
+ *
+ * <h3>Compare the CNN_2D info field with the CNN_1D field from the same sites in one VCF:</h3>
+ *
+ * <pre>
+ * gatk EvaluateInfoFieldConcordance \
+ *  -eval my.vcf \
+ *  -truth my.vcf \
+ *  -S summary.txt \
+ *  -eval-info-key CNN_2D \
+ *  -truth-info-key CNN_1D \
+ *  -epsilon 0.01
+ * </pre>
+ */
+@CommandLineProgramProperties(
+        summary=EvaluateInfoFieldConcordance.USAGE_SUMMARY,
+        oneLineSummary=EvaluateInfoFieldConcordance.USAGE_ONE_LINE_SUMMARY,
+        programGroup=VariantEvaluationProgramGroup.class)
+@DocumentedFeature
+@BetaFeature
+public class EvaluateInfoFieldConcordance extends AbstractConcordanceWalker {
+    static final String USAGE_ONE_LINE_SUMMARY = "Evaluate concordance of info fields in an input VCF against a validated truth VCF";
+    static final String USAGE_SUMMARY = "This tool evaluates info fields from an input VCF against a VCF that has been validated and is considered to represent ground truth.\n";
+    public static final String SUMMARY_LONG_NAME = "summary";
+    public static final String SUMMARY_SHORT_NAME = "S";
+
+    @Argument(doc="A table of summary statistics (true positives, sensitivity, etc.)", fullName=SUMMARY_LONG_NAME, shortName=SUMMARY_SHORT_NAME)
+    protected String summary;
+
+    @Argument(fullName="eval-info-key", shortName="eval-info-key", doc="Info key from eval vcf")
+    protected String evalInfoKey;
+
+    @Argument(fullName="truth-info-key", shortName="truth-info-key", doc="Info key from truth vcf")
+    protected String truthInfoKey;
+
+    @Advanced
+    @Argument(fullName="warn-big-differences",
+            shortName="warn-big-differences",
+            doc="If set differences in the info key values greater than epsilon will trigger warnings.",
+            optional=true)
+    protected boolean warnBigDifferences = false;
+
+    @Advanced
+    @Argument(fullName="epsilon", shortName="epsilon", doc="Difference tolerance", optional=true)
+    protected double epsilon = 0.1;
+
+    private int snpCount = 0;
+    private int indelCount = 0;
+
+    private double snpSumDelta = 0.0;
+    private double snpSumDeltaSquared = 0.0;
+    private double indelSumDelta = 0.0;
+    private double indelSumDeltaSquared = 0.0;
+
+    @Override
+    public void onTraversalStart() {
+        if(getEvalHeader().getInfoHeaderLine(evalInfoKey) == null){
+            throw new UserException("Missing key:"+evalInfoKey+" in Eval VCF:"+evalVariantsFile);
+        }
+
+        if(getTruthHeader().getInfoHeaderLine(truthInfoKey) == null){
+            throw new UserException("Missing key:"+truthInfoKey+" in Truth VCF:"+truthVariantsFile);
+        }
+    }
+
+    @Override
+    protected void apply(AbstractConcordanceWalker.TruthVersusEval truthVersusEval, ReadsContext readsContext, ReferenceContext refContext) {
+        ConcordanceState concordanceState = truthVersusEval.getConcordance();
+        switch (concordanceState) {
+            case TRUE_POSITIVE: {
+                if(truthVersusEval.getEval().isSNP()){
+                    snpCount++;
+                } else if (truthVersusEval.getEval().isIndel()) {
+                    indelCount++;
+                }
+                this.infoDifference(truthVersusEval.getEval(), truthVersusEval.getTruth());
+                break;
+            }
+            case FALSE_POSITIVE:
+            case FALSE_NEGATIVE:
+            case FILTERED_TRUE_NEGATIVE:
+            case FILTERED_FALSE_NEGATIVE: {
+                break;
+            }
+            default: {
+                throw new IllegalStateException("Unexpected ConcordanceState: " + concordanceState.toString());
+            }
+        }
+    }
+
+    private void infoDifference(final VariantContext eval, final VariantContext truth) {
+        if(eval.hasAttribute(this.evalInfoKey) && truth.hasAttribute(truthInfoKey)) {
+            final double evalVal = Double.valueOf((String) eval.getAttribute(this.evalInfoKey));
+            final double truthVal = Double.valueOf((String) truth.getAttribute(this.truthInfoKey));
+            final double delta = evalVal - truthVal;
+            final double deltaSquared = delta * delta;
+            if (eval.isSNP()) {
+                this.snpSumDelta += Math.sqrt(deltaSquared);
+                this.snpSumDeltaSquared += deltaSquared;
+            } else if (eval.isIndel()) {
+                this.indelSumDelta += Math.sqrt(deltaSquared);
+                this.indelSumDeltaSquared += deltaSquared;
+            }
+            if (warnBigDifferences && Math.abs(delta) > this.epsilon) {
+                this.logger.warn(String.format("Difference (%f) greater than epsilon (%f) at %s:%d %s:", delta, this.epsilon, eval.getContig(), eval.getStart(), eval.getAlleles().toString()));
+                this.logger.warn(String.format("\t\tTruth info: " + truth.getAttributes().toString()));
+                this.logger.warn(String.format("\t\tEval info: " + eval.getAttributes().toString()));
+            }
+        }
+    }
+
+    @Override
+    public Object onTraversalSuccess() {
+        final double snpMean = this.snpSumDelta / snpCount;
+        final double snpVariance = (this.snpSumDeltaSquared - this.snpSumDelta * this.snpSumDelta / snpCount) / snpCount;
+        final double snpStd = Math.sqrt(snpVariance);
+        final double indelMean = this.indelSumDelta / indelCount;
+        final double indelVariance = (this.indelSumDeltaSquared - this.indelSumDelta * this.indelSumDelta / indelCount) / indelCount;
+        final double indelStd = Math.sqrt(indelVariance);
+
+        this.logger.info(String.format("SNP average delta %f and standard deviation: %f", snpMean, snpStd));
+        this.logger.info(String.format("INDEL average delta %f and standard deviation: %f", indelMean, indelStd));
+
+        try (final InfoConcordanceRecord.InfoConcordanceWriter
+                     concordanceWriter = InfoConcordanceRecord.getWriter(Paths.get(this.summary))){
+            concordanceWriter.writeRecord(new InfoConcordanceRecord(VariantContext.Type.SNP, this.evalInfoKey, this.truthInfoKey, snpMean, snpStd));
+            concordanceWriter.writeRecord(new InfoConcordanceRecord(VariantContext.Type.INDEL, this.evalInfoKey, this.truthInfoKey, indelMean, indelStd));
+        } catch (IOException e) {
+            throw new UserException("Encountered an IO exception writing the concordance summary table", e);
+        }
+
+        return "SUCCESS";
+    }
+
+    @Override
+    protected boolean areVariantsAtSameLocusConcordant(VariantContext truth, VariantContext eval) {
+        final boolean sameRefAllele = truth.getReference().equals(eval.getReference());
+        final boolean containsAltAllele = eval.getAlternateAlleles().contains(truth.getAlternateAllele(0));
+        return sameRefAllele && containsAltAllele;
+    }
+
+    @Override
+    protected Predicate<VariantContext> makeTruthVariantFilter() {
+        return vc -> !vc.isFiltered() && !vc.isSymbolicOrSV();
+    }
+
+    @Override
+    protected Predicate<VariantContext> makeEvalVariantFilter() {
+        return vc -> !vc.isFiltered() && !vc.isSymbolicOrSV();
+    }
+
+}

src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/InfoConcordanceRecord.java

@@ -0,0 +1,140 @@
+package org.broadinstitute.hellbender.tools.walkers.validation;
+
+import htsjdk.variant.variantcontext.VariantContext;
+
+import java.io.IOException;
+import java.nio.file.Path;
+
+import org.broadinstitute.hellbender.exceptions.UserException;
+
+import org.broadinstitute.hellbender.utils.tsv.DataLine;
+import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection;
+import org.broadinstitute.hellbender.utils.tsv.TableWriter;
+import org.broadinstitute.hellbender.utils.tsv.TableReader;
+
+/**
+ * Keeps track of concordance between two info fields.
+ */
+public class InfoConcordanceRecord {
+    private static final String VARIANT_TYPE_COLUMN_NAME = "type";
+    private static final String EVAL_INFO_KEY = "eval_info_key";
+    private static final String TRUE_INFO_KEY = "true_info_key";
+    private static final String MEAN_DIFFERENCE = "mean_difference";
+    private static final String STD_DIFFERENCE = "std_difference";
+    private static final String[] INFO_CONCORDANCE_COLUMN_HEADER =
+            {VARIANT_TYPE_COLUMN_NAME, EVAL_INFO_KEY, TRUE_INFO_KEY, MEAN_DIFFERENCE, STD_DIFFERENCE};
+    final VariantContext.Type type;
+    private final String evalKey;
+    private final String trueKey;
+    private final double mean;
+    private final double std;
+
+    /**
+     * Record keeps track of concordance between values from INFO-field keys of a VCF.
+     *
+     * @param type SNP or INDEL
+     * @param evalKey The INFO field key from the eval VCF
+     * @param trueKey The INFO field key from the truth VCF
+     * @param mean The mean of the differences in values for these INFO fields.
+     * @param std The standard deviation of the differences in values for these INFO fields.
+     */
+    public InfoConcordanceRecord(VariantContext.Type type, String evalKey, String trueKey, double mean, double std) {
+        this.type = type;
+        this.evalKey = evalKey;
+        this.trueKey = trueKey;
+        this.mean = mean;
+        this.std = std;
+    }
+
+    /**
+     *
+     * @return Variant type (e.g. SNP or INDEL)
+     */
+    public VariantContext.Type getVariantType() {
+        return this.type;
+    }
+
+    /**
+     *
+     * @return The mean of the differences between two INFO fields
+     */
+    public double getMean() {
+        return this.mean;
+    }
+
+    /**
+     *
+     * @return The Standard Deviation of the differences between two INFO fields
+     */
+    public double getStd() {
+        return this.std;
+    }
+
+    /**
+     *
+     * @return The INFO field for the eval VCF
+     */
+    public String getEvalKey() {
+        return this.evalKey;
+    }
+
+    /**
+     *
+     * @return The INFO field for the truth VCF
+     */
+    public String getTrueKey() {
+        return this.trueKey;
+    }
+
+    /**
+     * Get a table writer
+     * @param outputTable A Path where the output table will be written
+     * @return A Table writer for INFO field concordances
+     */
+    public static InfoConcordanceWriter getWriter(Path outputTable) {
+        try {
+            InfoConcordanceWriter writer = new InfoConcordanceWriter(outputTable);
+            return writer;
+        }
+        catch (IOException e) {
+            throw new UserException(String.format("Encountered an IO exception while writing from %s.", outputTable), e);
+        }
+    }
+
+    /**
+     * Table writing class for InfoConcordanceRecords
+     */
+    public static class InfoConcordanceWriter extends TableWriter<InfoConcordanceRecord> {
+        private InfoConcordanceWriter(Path output) throws IOException {
+            super(output.toFile(), new TableColumnCollection(INFO_CONCORDANCE_COLUMN_HEADER));
+        }
+
+        @Override
+        protected void composeLine(InfoConcordanceRecord record, DataLine dataLine) {
+            dataLine.set(VARIANT_TYPE_COLUMN_NAME, record.getVariantType().toString())
+                    .set(EVAL_INFO_KEY, record.getEvalKey())
+                    .set(TRUE_INFO_KEY, record.getTrueKey())
+                    .set(MEAN_DIFFERENCE, record.getMean())
+                    .set(STD_DIFFERENCE, record.getStd());
+        }
+    }
+
+    /**
+     * Table reading class for InfoConcordanceRecords
+     */
+    public static class InfoConcordanceReader extends TableReader<InfoConcordanceRecord> {
+        public InfoConcordanceReader(Path summary) throws IOException {
+            super(summary.toFile());
+        }
+
+        @Override
+        protected InfoConcordanceRecord createRecord(DataLine dataLine) {
+            VariantContext.Type type = VariantContext.Type.valueOf(dataLine.get(VARIANT_TYPE_COLUMN_NAME));
+            String evalKey = dataLine.get(EVAL_INFO_KEY);
+            String trueKey = dataLine.get(TRUE_INFO_KEY);
+            double mean = Double.parseDouble(dataLine.get(MEAN_DIFFERENCE));
+            double std = Double.parseDouble(dataLine.get(STD_DIFFERENCE));
+            return new InfoConcordanceRecord(type, evalKey, trueKey, mean, std);
+        }
+    }
+}