zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Annotator now buffers indel calls (prevents double-output from double-calls to map) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3413 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-05-21 16:34:34 +00:00
parent 4e834b5e35
commit 7fb3f2d3eb
1 changed files with 21 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

21
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -82,6 +82,8 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
private VariantAnnotatorEngine engine; private VariantAnnotatorEngine engine;
private Collection<VariantContext> indelBufferContext;
private void listAnnotationsAndExit() { private void listAnnotationsAndExit() {
List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class); List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class);
@ -139,6 +141,10 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
vcfWriter = new VCFWriter(out); vcfWriter = new VCFWriter(out);
VCFHeader vcfHeader = new VCFHeader(hInfo, samples); VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader); vcfWriter.writeHeader(vcfHeader);
if ( indelsOnly ) {
indelBufferContext = null;
}
} }
/** /**
@ -199,11 +205,24 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
} }
} }
if ( variant instanceof VCFRecord) { if ( ! indelsOnly ) {
if ( variant instanceof VCFRecord ) {
for(VariantContext annotatedVC : annotatedVCs ) { for(VariantContext annotatedVC : annotatedVCs ) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase())); vcfWriter.addRecord(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase()));
} }
} }
} else {
// check to see if the buffered context is different (in location) this context
if ( indelBufferContext != null && ! indelBufferContext.iterator().next().getLocation().equals(annotatedVCs.iterator().next().getLocation()) ) {
for(VariantContext annotatedVC : indelBufferContext ) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase()));
}
indelBufferContext = annotatedVCs;
} else {
indelBufferContext = annotatedVCs;
}
}
return 1; return 1;
} }