From d82d6c0665a1b3e9524619805f32a0f67fd9a035 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 9 Sep 2009 17:34:16 +0000
Subject: [PATCH] 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
---
 .../filters/VECLodThresholdByCoverage.java    | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThresholdByCoverage.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThresholdByCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThresholdByCoverage.java
new file mode 100755
index 000000000..d9d00431f
--- /dev/null
+++ b/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;
+    }
+}