From 7b2a7cfbe763cfa8aeca37205dfe9b1ffedee094 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 14 Nov 2011 14:31:27 -0500 Subject: [PATCH] Transfer headers from the resource VCF when possible when using expressions. While there, VA was modified so that it didn't assume that the ID field was present in the VC's info map in preparation for Mark's upcoming changes. --- .../walkers/annotator/VariantAnnotator.java | 25 +++++++++++++++++-- .../annotator/VariantAnnotatorEngine.java | 23 +++++++++++------ .../VariantAnnotatorIntegrationTest.java | 2 +- 3 files changed, 39 insertions(+), 11 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index ea11391d9..20e72dd57 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -222,8 +222,29 @@ public class VariantAnnotator extends RodWalker 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 ) + 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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index e4bc0d5d5..20f28007a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -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 binding; - public VAExpression(String fullEpression, List> bindings) { - int indexOfDot = fullEpression.lastIndexOf("."); + public VAExpression(String fullExpression, List> 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 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 getRequestedExpressions() { return requestedExpressions; } + private void initializeAnnotations(List annotationGroupsToUse, List annotationsToUse, List 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)); + } } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 189f643d4..bde4c4a8f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -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); }