From f89a89ffe34d76447a2415dfa004d4e984594be0 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 8 Oct 2009 16:07:45 +0000
Subject: [PATCH] Use of AlleleFrequency as an input to PowerAndCoverage is
 deprecated by the new walker. Reverting to the standard "power at 1 allele"
 calculation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1788 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/poolseq/PowerAndCoverageWalker.java      | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerAndCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerAndCoverageWalker.java
index efdf27ce7..8e23de3e1 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerAndCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerAndCoverageWalker.java
@@ -51,9 +51,6 @@ public class PowerAndCoverageWalker extends LocusWalker<SQuad<Integer>, SQuad<Lo
     @Argument(fullName="poolSize", shortName="ps", doc="Number of individuals in the pool", required = true)
     public int numIndividuals = 0;
 
-    @Argument(fullName="alleleFrequency", shortName="af", doc="Calculate power for this many alleles in the pool", required=false)
-    public int alleleFreq = 1;
-
     protected PrintStream outputWriter = null;
 
     public void initialize() {
@@ -61,9 +58,6 @@ public class PowerAndCoverageWalker extends LocusWalker<SQuad<Integer>, SQuad<Lo
             throw new StingException("Pool size must be greater than 1. You input "+numIndividuals);
         }
 
-        if ( alleleFreq > 2*numIndividuals ) {
-            throw new StingException("Allele frequency must be less than the number of alleles in the pool");
-        }
         if( outputFile != null ) {
             try {
                 outputWriter = new PrintStream(outputFile);
@@ -262,7 +256,7 @@ public class PowerAndCoverageWalker extends LocusWalker<SQuad<Integer>, SQuad<Lo
     }
 
     private double getSNPProportion() {
-        return alleleFreq/(2.0*numIndividuals);
+        return 1/(2.0*numIndividuals);
     }
 
 }