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Make VA annotate dbsnp again 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-05-11 14:06:53 +00:00
parent b09e7231d1
commit 572b383fe2
2 changed files with 5 additions and 4 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -185,7 +185,7 @@ public class VariantAnnotatorEngine {
DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)); DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
infoAnnotations.put(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1"); infoAnnotations.put(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1");
// annotate dbsnp id if available and not already there // annotate dbsnp id if available and not already there
if ( dbsnp != null && !vc.hasAttribute("ID") ) if ( dbsnp != null && (!vc.hasAttribute("ID") || vc.getAttribute("ID").equals(VCFRecord.EMPTY_ID_FIELD)) )
infoAnnotations.put("ID", dbsnp.getRsID()); infoAnnotations.put("ID", dbsnp.getRsID());
} }
@ -199,10 +199,11 @@ public class VariantAnnotatorEngine {
infoAnnotations.put(VCFRecord.HAPMAP3_KEY, hapmap3.size() == 0 ? "0" : "1"); infoAnnotations.put(VCFRecord.HAPMAP3_KEY, hapmap3.size() == 0 ? "0" : "1");
} }
//Process the info field //Process the info field
List<Map<String, Object>> infoAnnotationOutputsList = new LinkedList<Map<String, Object>>(); //each element in infoAnnotationOutputs corresponds to a single line in the output VCF file List<Map<String, Object>> infoAnnotationOutputsList = new LinkedList<Map<String, Object>>(); //each element in infoAnnotationOutputs corresponds to a single line in the output VCF file
infoAnnotationOutputsList.add(new HashMap<String, Object>(vc.getAttributes())); //keep the existing info-field annotations. After this infoAnnotationOutputsList.size() == 1, which means the output VCF file gains 1 line. infoAnnotationOutputsList.add(new HashMap<String, Object>(vc.getAttributes())); //keep the existing info-field annotations. After this infoAnnotationOutputsList.size() == 1, which means the output VCF file gains 1 line.
// put the DB membership info in
infoAnnotationOutputsList.get(0).putAll(infoAnnotations);
//go through all the requested info annotationTypes //go through all the requested info annotationTypes
for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations )
@ -266,7 +267,7 @@ public class VariantAnnotatorEngine {
} }
} }
//Create a separate VariantContext (aka. output line) for each element in infoAnnotationOutputsList //Create a separate VariantContext (aka. output line) for each element in infoAnnotationOutputsList
Collection<VariantContext> returnValue = new LinkedList<VariantContext>(); Collection<VariantContext> returnValue = new LinkedList<VariantContext>();
for(Map<String, Object> infoAnnotationOutput : infoAnnotationOutputsList) { for(Map<String, Object> infoAnnotationOutput : infoAnnotationOutputsList) {
returnValue.add( new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), infoAnnotationOutput) ); returnValue.add( new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), infoAnnotationOutput) );

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java
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@ -26,7 +26,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
*/ */
String[] md5WithDashSArg = {"c5bcbad4f4bb8455eea46c1a51a77d2a"}; String[] md5WithDashSArg = {"fb6f52b72610a4f6bcf4c130ec14705a"};
WalkerTestSpec specWithSArg = new WalkerTestSpec( WalkerTestSpec specWithSArg = new WalkerTestSpec(
"-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " + "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " +
"-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " + "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " +