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

This commit is contained in:
Guillermo del Angel 2011-11-14 15:00:03 -05:00
parent f1db31f072 4dc9dbe890
commit 5c38a9cfd6
3 changed files with 43 additions and 11 deletions
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29
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -222,8 +222,33 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
if ( isUniqueHeaderLine(line, hInfo) )
hInfo.add(line);
}
for ( String expression : expressionsToUse )
hInfo.add(new VCFInfoHeaderLine(expression, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Value transferred from another external VCF resource"));
// for the expressions, pull the info header line from the header of the resource rod
for ( VariantAnnotatorEngine.VAExpression expression : engine.getRequestedExpressions() ) {
// special case the ID field
if ( expression.fieldName.equals("ID") ) {
hInfo.add(new VCFInfoHeaderLine(expression.fullName, 1, VCFHeaderLineType.String, "ID field transferred from external VCF resource"));
continue;
}
VCFInfoHeaderLine targetHeaderLine = null;
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
if ( line instanceof VCFInfoHeaderLine ) {
VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
if ( infoline.getName().equals(expression.fieldName) ) {
targetHeaderLine = infoline;
break;
}
}
}
if ( targetHeaderLine != null ) {
if ( targetHeaderLine.getCountType() == VCFHeaderLineCount.INTEGER )
hInfo.add(new VCFInfoHeaderLine(expression.fullName, targetHeaderLine.getCount(), targetHeaderLine.getType(), targetHeaderLine.getDescription()));
else
hInfo.add(new VCFInfoHeaderLine(expression.fullName, targetHeaderLine.getCountType(), targetHeaderLine.getType(), targetHeaderLine.getDescription()));
} else {
hInfo.add(new VCFInfoHeaderLine(expression.fullName, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Value transferred from another external VCF resource"));
}
}
engine.invokeAnnotationInitializationMethods(hInfo);

23
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -49,20 +49,20 @@ public class VariantAnnotatorEngine {
private AnnotatorCompatibleWalker walker;
private GenomeAnalysisEngine toolkit;
private static class VAExpression {
protected static class VAExpression {
public String fullName, fieldName;
public RodBinding<VariantContext> binding;
public VAExpression(String fullEpression, List<RodBinding<VariantContext>> bindings) {
int indexOfDot = fullEpression.lastIndexOf(".");
public VAExpression(String fullExpression, List<RodBinding<VariantContext>> bindings) {
int indexOfDot = fullExpression.lastIndexOf(".");
if ( indexOfDot == -1 )
throw new UserException.BadArgumentValue(fullEpression, "it should be in rodname.value format");
throw new UserException.BadArgumentValue(fullExpression, "it should be in rodname.value format");
fullName = fullEpression;
fieldName = fullEpression.substring(indexOfDot+1);
fullName = fullExpression;
fieldName = fullExpression.substring(indexOfDot+1);
String bindingName = fullEpression.substring(0, indexOfDot);
String bindingName = fullExpression.substring(0, indexOfDot);
for ( RodBinding<VariantContext> rod : bindings ) {
if ( rod.getName().equals(bindingName) ) {
binding = rod;
@ -97,6 +97,8 @@ public class VariantAnnotatorEngine {
requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
}
protected List<VAExpression> getRequestedExpressions() { return requestedExpressions; }
private void initializeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude) {
AnnotationInterfaceManager.validateAnnotations(annotationGroupsToUse, annotationsToUse);
requestedInfoAnnotations = AnnotationInterfaceManager.createInfoFieldAnnotations(annotationGroupsToUse, annotationsToUse);
@ -211,8 +213,13 @@ public class VariantAnnotatorEngine {
continue;
VariantContext vc = VCs.iterator().next();
if ( vc.hasAttribute(expression.fieldName) )
// special-case the ID field
if ( expression.fieldName.equals("ID") ) {
if ( vc.hasID() )
infoAnnotations.put(expression.fullName, vc.getID());
} else if ( vc.hasAttribute(expression.fieldName) ) {
infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
}
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpressionWithID() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
Arrays.asList("4a6f0675242f685e9072c1da5ad9e715"));
Arrays.asList("1b4921085b26cbfe07d53b7c947de1e5"));
executeTest("using expression with ID", spec);
}