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Commented out the generation of the GATKReport that I was using for debugging. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5903 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-05-27 22:15:09 +00:00
parent 2a9c75c5ba
commit b4d379584c
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java
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@ -243,6 +243,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
double norm = 0.0; double norm = 0.0;
/*
GATKReport report = new GATKReport(); GATKReport report = new GATKReport();
report.addTable("TransmissionProbability", "Reports various quantities used to compute transmission probability"); report.addTable("TransmissionProbability", "Reports various quantities used to compute transmission probability");
@ -255,6 +256,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
table.addColumn("child", "unknown"); table.addColumn("child", "unknown");
table.addColumn("childProbability", "unknown"); table.addColumn("childProbability", "unknown");
table.addColumn("configLikelihood", "unknown"); table.addColumn("configLikelihood", "unknown");
*/
for (Genotype momGenotype : possibleMomGenotypes) { for (Genotype momGenotype : possibleMomGenotypes) {
for (Genotype dadGenotype : possibleDadGenotypes) { for (Genotype dadGenotype : possibleDadGenotypes) {
@ -271,6 +273,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
bestChildGenotype = childGenotype; bestChildGenotype = childGenotype;
} }
/*
String config = momGenotype.toString() + dadGenotype.toString() + childGenotype.toString(); String config = momGenotype.toString() + dadGenotype.toString() + childGenotype.toString();
double[] momLikelihoods = MathUtils.normalizeFromLog10(momGenotype.getLikelihoods().getAsVector()); double[] momLikelihoods = MathUtils.normalizeFromLog10(momGenotype.getLikelihoods().getAsVector());
@ -292,6 +295,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
table.set(config, "childProbability", childProbability); table.set(config, "childProbability", childProbability);
table.set(config, "configLikelihood", prior*configurationLikelihood); table.set(config, "configLikelihood", prior*configurationLikelihood);
*/
} }
} }
} }