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comments for eric 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2035 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-11-13 14:19:31 +00:00
parent 234bb71747
commit cff31f2d06
2 changed files with 22 additions and 2 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
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@ -45,6 +45,18 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
if ( contexts == null )
return null;
// todo -- eric, can you refactor this into a superclass the manages the i over 2n calculation?
//
// The only thing that's different from pools and msg should be the calls to
// initializeGenotypeLikelihoods and calculateAlleleFrequencyPosteriors
// There's a lot of functionality here that can be separated into a superclass that requires
// a few methods be overridden and it'll magically work for all data types, etc.
//
// Here are some examples:
// getNumberSamples() ->
// likelihoodsOfDGivenF() -> for MSG, pools, etc -- see below
//
initializeAlleleFrequencies(contexts.size());
// run joint estimation for the full GL contexts
@ -123,7 +135,14 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
log10PofDgivenAFi[baseIndex] = new double[frequencyEstimationPoints];
}
DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
//
// todo -- if you invert this loop
// foreach frequnecy
// foreach altAllele
//
// then the pooled vs. msg calculation is just a function call difference
// for each minor allele frequency
for (int i = 0; i < frequencyEstimationPoints; i++) {
double f = (double)i / (double)(frequencyEstimationPoints-1);
@ -162,6 +181,7 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
}
}
// todo -- shouldn't this be in a function for clarity?
// for each alternate allele
for ( char altAllele : BaseUtils.BASES ) {
if ( altAllele == ref )

2
java/src/org/broadinstitute/sting/utils/GATKErrorReport.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GATKArgumentCollection;
import org.simpleframework.xml.Element;
import org.simpleframework.xml.ElementList;
import org.simpleframework. xml.ElementList;
import org.simpleframework.xml.Serializer;
import org.simpleframework.xml.core.Persister;
import org.simpleframework.xml.stream.Format;