From dec713a184be78f4a14b49d08744ca0b9fb9b663 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 Aug 2010 05:06:16 +0000
Subject: [PATCH] Simple test code from Steve Schaffner to compute R^2 and D'. 
 This is just for educational purposes.  Don't use this code for anything,
 ever!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4080 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../haplotype/ComputeRSquaredAndDPrime.java   | 88 +++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/oneoffprojects/walkers/haplotype/ComputeRSquaredAndDPrime.java

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/haplotype/ComputeRSquaredAndDPrime.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/haplotype/ComputeRSquaredAndDPrime.java
new file mode 100755
index 000000000..d2fbd26da
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/haplotype/ComputeRSquaredAndDPrime.java
@@ -0,0 +1,88 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.haplotype;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+import java.io.PrintStream;
+
+/**
+ * A very simple code snippet from Steve Schaffner that computs R^2 and D' given observed counts for
+ * AA, Aa, aA, and aa genotypes.  This code is meant only to be instructive.  Do not use this for
+ * anything, ever!
+ */
+public class ComputeRSquaredAndDPrime extends RodWalker<Integer, Integer> {
+    @Argument(fullName="AA", shortName="AA", doc="Number of counts for AA genotype") public Integer AA;
+    @Argument(fullName="Aa", shortName="Aa", doc="Number of counts for Aa genotype") public Integer Aa;
+    @Argument(fullName="aA", shortName="aA", doc="Number of counts for aA genotype") public Integer aA;
+    @Argument(fullName="aa", shortName="aa", doc="Number of counts for aa genotype") public Integer aa;
+
+    @Output
+    private PrintStream out;
+
+    public void initialize() {
+        int i, j;
+        Integer[][] hap = new Integer[2][2];
+        for (int k = 0; k < 2; k++) {
+            hap[k] = new Integer[2];
+        }
+
+        hap[0][0] = AA;
+        hap[0][1] = Aa;
+        hap[1][0] = aA;
+        hap[1][1] = aa;
+
+        Integer[] colTot = new Integer[2];
+        Integer[] rowTot = new Integer[2];
+        double prod, dprime, f1, f2, ddenom, r2;
+
+        for (i = 0; i < 2; i++) { rowTot[i] = colTot[i] = 0; }
+        for (i = 0; i < 2; i++) {
+            for (j = 0; j < 2; j++) {
+                rowTot[j] += hap[i][j];
+                colTot[i] += hap[i][j];
+            }
+        }
+        prod = rowTot[0] * rowTot[1] * colTot[0] * colTot[1];
+
+        if (prod == 0) {
+            out.println("Missing data");
+            System.exit(1);
+        }
+        dprime = hap[0][0] * hap[1][1] - hap[0][1] * hap[1][0];
+        if (dprime > 0) {
+            f1 = rowTot[0] * colTot[1];
+            f2 = rowTot[1] * colTot[0];
+            ddenom = (f1 > f2) ? f2 : f1;
+        } else {
+            f1 = rowTot[0] * colTot[0];
+            f2 = rowTot[1] * colTot[1];
+            ddenom = (f1 > f2) ? f2 : f1;
+        }
+        r2 = dprime * dprime / prod;
+        dprime /= ddenom;
+
+        out.printf("r2: %.5f%n", r2);
+        out.printf("D': %.5f%n", dprime);
+
+        System.exit(0);
+    }
+
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return null;
+    }
+
+    @Override
+    public Integer reduceInit() {
+        return null;
+    }
+
+    @Override
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+}