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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mauricio Carneiro 2011-07-26 19:29:45 -04:00
parent 321afac4e8 405e521d44
commit 20a3b31b61
3 changed files with 11 additions and 9 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -234,7 +234,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
finalGenotypes.add(father);
finalGenotypes.add(child);
if (mother.isCalled() && father.isCalled() && child.isCalled() && !(mother.isHet() && father.isHet() && child.isHet())) {
if (mother.isCalled() && father.isCalled() && child.isCalled()) {
ArrayList<Genotype> possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother);
ArrayList<Genotype> possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father);
ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child);
@ -265,12 +265,14 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
}
}
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.putAll(bestChildGenotype.getAttributes());
attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
bestChildGenotype = Genotype.modifyAttributes(bestChildGenotype, attributes);
if (!(bestMotherGenotype.isHet() && bestFatherGenotype.isHet() && bestChildGenotype.isHet())) {
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.putAll(bestChildGenotype.getAttributes());
attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
bestChildGenotype = Genotype.modifyAttributes(bestChildGenotype, attributes);
finalGenotypes = getPhasedGenotypes(bestMotherGenotype, bestFatherGenotype, bestChildGenotype);
finalGenotypes = getPhasedGenotypes(bestMotherGenotype, bestFatherGenotype, bestChildGenotype);
}
}
return finalGenotypes;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -67,7 +67,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
@Argument(fullName="stratificationModule", shortName="ST", doc="One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)", required=false)
protected String[] STRATIFICATIONS_TO_USE = {};
@Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)")
@Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)", required=false)
protected Boolean NO_STANDARD_STRATIFICATIONS = false;
@Argument(fullName="onlyVariantsOfType", shortName="VT", doc="If provided, only variants of these types will be considered during the evaluation, in ", required=false)
@ -77,7 +77,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
@Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)", required=false)
protected String[] MODULES_TO_USE = {};
@Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)")
@Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)", required=false)
protected Boolean NO_STANDARD_MODULES = false;
// Other arguments

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
View File

@ -20,7 +20,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("ff02b1583ee3a12ed66a9c0e08e346b2")
Arrays.asList("45fef0e23113e2fcd9570379e2fc1b75")
);
executeTest("testBasicFunctionality", spec);
}