Excludes variants that fall below a certain LOD that changes as a function of depth.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1564 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThresholdByCoverage.java

@@ -0,0 +1,39 @@
+package org.broadinstitute.sting.gatk.walkers.filters;
+
+import java.util.HashMap;
+
+public class VECLodThresholdByCoverage implements VariantExclusionCriterion {
+    private double slope = 0.46;
+    private double depth;
+    private double lod;
+    private boolean exclude;
+
+    public void initialize(HashMap<String, String> arguments) {
+        if (arguments.get("slope") != null) {
+            slope = Double.valueOf(arguments.get("slope"));
+        }
+    }
+
+    public void compute(VariantContextWindow contextWindow) {
+        depth = (double) contextWindow.getContext().getVariant().getPileupDepth();
+        lod = contextWindow.getContext().getVariant().getLodBtr();
+
+        exclude = (lod < slope*depth);
+    }
+
+    public double inclusionProbability() {
+        return exclude ? 0.0 : 1.0;
+    }
+
+    public String getStudyHeader() {
+        return String.format("LodThresholdByCoverage(%f)\tdepth\tlod", slope);
+    }
+
+    public String getStudyInfo() {
+        return String.format("%s\t%d\t%f", exclude ? "fail" : "pass", (int) depth, lod);
+    }
+
+    public boolean useZeroQualityReads() {
+        return false;
+    }
+}