javadoc

broadinstitute · Aug 8, 2018 · 30a4073 · 30a4073
1 parent d33f9f7
commit 30a4073
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilteringFirstPass.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilteringFirstPass.java
@@ -7,6 +7,7 @@
 import org.apache.commons.lang3.tuple.Pair;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.Utils;
+import org.broadinstitute.hellbender.utils.param.ParamUtils;
 import org.broadinstitute.hellbender.utils.tsv.DataLine;
 import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection;
 import org.broadinstitute.hellbender.utils.tsv.TableWriter;
@@ -16,6 +17,10 @@
 import java.io.IOException;
 import java.util.*;
 
+/**
+ * Stores the results of the first pass of {@link FilterMutectCalls}, a purely online step in which each variant is
+ * not "aware" of other variants, and learns various global properties necessary for a more refined second step.
+ */
 public class FilteringFirstPass {
     final List<FilterResult> filterResults;
     final Map<String, ImmutablePair<String, Integer>> filteredPhasedCalls;
@@ -92,6 +97,7 @@ public void learnModelForSecondPass(final double requestedFPR){
      * @return
      */
     public static FilterStats calculateThresholdForReadOrientationFilter(final double[] posteriors, final double requestedFPR){
+        ParamUtils.isPositive(requestedFPR, "requested FPR must be positive");
         final double thresholdForFilteringNone = 1.0;
         final double thresholdForFilteringAll = 0.0;