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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
This commit is contained in:
chartl 2009-10-08 16:07:45 +00:00
parent ae05f5c7ad
commit f89a89ffe3
1 changed files with 1 additions and 7 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerAndCoverageWalker.java
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@ -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) @Argument(fullName="poolSize", shortName="ps", doc="Number of individuals in the pool", required = true)
public int numIndividuals = 0; 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; protected PrintStream outputWriter = null;
public void initialize() { 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); 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 ) { if( outputFile != null ) {
try { try {
outputWriter = new PrintStream(outputFile); outputWriter = new PrintStream(outputFile);
@ -262,7 +256,7 @@ public class PowerAndCoverageWalker extends LocusWalker<SQuad<Integer>, SQuad<Lo
} }
private double getSNPProportion() { private double getSNPProportion() {
return alleleFreq/(2.0*numIndividuals); return 1/(2.0*numIndividuals);
} }
} }