Adds a class to represent expected insert-size distribution (normal a…

scripts/sv/run_whole_pipeline.sh

@@ -69,6 +69,7 @@ case ${GATK_SV_TOOL} in
             --breakpoint-intervals ${PROJECT_OUTPUT_DIR}/intervals \
             --high-coverage-intervals "${PROJECT_OUTPUT_DIR}/highCoverageIntervals.bed" \
             --fastq-dir ${PROJECT_OUTPUT_DIR}/fastq \
+	    --read-metadata ${PROJECT_OUTPUT_DIR}/read-metadata.txt \
             --contig-sam-file ${PROJECT_OUTPUT_DIR}/assemblies.bam \
             --target-link-file ${PROJECT_OUTPUT_DIR}/target_links.bedpe \
             --exp-interpret"

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/InsertSizeDistribution.java

@@ -0,0 +1,122 @@
+package org.broadinstitute.hellbender.tools.spark.sv;
+
+import org.apache.commons.math3.distribution.AbstractIntegerDistribution;
+import org.apache.commons.math3.distribution.IntegerDistribution;
+import org.broadinstitute.hellbender.exceptions.UserException;
+
+import java.io.Serializable;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Holds the information characterizing and insert size distribution.
+ */
+public class InsertSizeDistribution implements Serializable {
+
+    private static final long serialVersionUID = 1L;
+
+    private static Pattern DESCRIPTION_PATTERN =
+            Pattern.compile("^\\s*(?<name>[^\\s\\(\\)]+)\\s*\\((?<mean>[^,\\(\\)]+?)\\s*(?:,\\s*(?<stddev>[^,\\(\\)]+?)\\s*)?\\)\\s*");
+
+    private final String description;
+
+    private transient AbstractIntegerDistribution dist;
+
+    private AbstractIntegerDistribution dist() {
+        initializeDistribution();
+        return dist;
+    }
+
+    public double mean() {
+        return dist().getNumericalMean();
+    }
+
+    public double variance() { return dist().getNumericalVariance(); }
+
+    public double stddev() { return Math.sqrt(variance()); }
+
+    public InsertSizeDistribution(final String distrString) {
+        this.description = distrString;
+        initializeDistribution();
+    }
+
+    private void initializeDistribution() {
+        if (!description.matches(DESCRIPTION_PATTERN.pattern())) {
+            throw new UserException.BadInput("unsupported insert size distribution description format: " + description);
+        }
+        final Matcher matcher = DESCRIPTION_PATTERN.matcher(description);
+        if (!matcher.find()) {
+            throw new UserException.BadInput("the insert-size distribution spec is not up to standard: " + description);
+        }
+        final String nameString = matcher.group("name");
+        final String meanString = matcher.group("mean");
+        final String stddevString = matcher.group("stddev");
+        final InsertSizeDistributionShape type = extractDistributionShape(nameString, description);
+        if (stddevString != null) {
+            final double mean = extractDoubleParameter("mean", description, meanString, 0, Double.MAX_VALUE);
+            final double stddev = extractDoubleParameter("stddev", description, stddevString, 0, Double.MAX_VALUE);
+            dist = type.fromMeanAndStdDeviation(mean, stddev);
+        } else {
+            dist = type.fromReadMetadataFile(meanString);
+        }
+    }
+
+    private static InsertSizeDistributionShape extractDistributionShape(final String nameString, final String description) {
+        final InsertSizeDistributionShape result = InsertSizeDistributionShape.decode(nameString);
+        if (result == null) {
+            throw new UserException.BadInput("unsupported insert size distribution name '" + nameString
+                    + "' in description: " + description);
+        }
+        return result;
+    }
+
+    private static double extractDoubleParameter(final String name, final String description,
+                                                       final String valueString, final double min,
+                                                       final double max) {
+        final double value;
+        try {
+            value = Double.parseDouble(valueString);
+        } catch (final NumberFormatException ex) {
+            throw new UserException.BadInput("bad " + name + " string '" + valueString + "' in insert size distribution description: "  + description);
+        }
+        if (value < min || Double.isInfinite(value) || Double.isNaN(value) || value > max) {
+            throw new UserException.BadInput("bad " + name + " value '" + value + "' in insert size distribution description: " + description);
+        }
+        return value;
+    }
+
+    @Override
+    public String toString() {
+        return description;
+    }
+
+    @Override
+    public int hashCode() {
+        return dist().hashCode();
+    }
+
+    @Override
+    public boolean equals(final Object obj) {
+        if (!(obj instanceof InsertSizeDistribution)) {
+            return false;
+        } else {
+            return ((InsertSizeDistribution)obj).dist().equals(dist());
+        }
+    }
+
+    public int minimum() {
+        return Math.max(0, dist().getSupportLowerBound());
+    }
+
+    public int maximum() {
+        return Math.min(Integer.MAX_VALUE, dist().getSupportUpperBound());
+    }
+
+    public double probability(final int size) {
+        return dist().probability(size);
+    }
+
+    public double logProbability(final int size) {
+        return dist().logProbability(size);
+    }
+}