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Move to 4.0 and away from VCFRecord. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3780 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-13 15:54:54 +00:00
parent 6442dabf94
commit 9a05e8143d
2 changed files with 14 additions and 15 deletions
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27
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
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@ -43,7 +43,6 @@ import java.util.Map.Entry;
import org.broad.tribble.vcf.VCFHeader; import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine; import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -74,7 +73,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
//@Allows(value={DataSource.READS, DataSource.REFERENCE}) //@Allows(value={DataSource.READS, DataSource.REFERENCE})
//@Reference(window=@Window(start=-50,stop=50)) //@Reference(window=@Window(start=-50,stop=50))
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedList<VCFRecord>> implements TreeReducible<LinkedList<VCFRecord>> { public class GenomicAnnotator extends RodWalker<LinkedList<VariantContext>, LinkedList<VariantContext>> implements TreeReducible<LinkedList<VariantContext>> {
@Argument(fullName="vcfOutput", shortName="vcf", doc="VCF file to which all variants should be written with annotations", required=true) @Argument(fullName="vcfOutput", shortName="vcf", doc="VCF file to which all variants should be written with annotations", required=true)
protected File VCF_OUT; protected File VCF_OUT;
@ -239,7 +238,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName())); hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName()));
hInfo.addAll(engine.getVCFAnnotationDescriptions()); hInfo.addAll(engine.getVCFAnnotationDescriptions());
vcfWriter = new VCFWriter(VCF_OUT); vcfWriter = new VCFWriter(VCF_OUT, true);
VCFHeader vcfHeader = new VCFHeader(hInfo, samples); VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader); vcfWriter.writeHeader(vcfHeader);
} }
@ -249,7 +248,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
* *
* @return 0 * @return 0
*/ */
public LinkedList<VCFRecord> reduceInit() { return new LinkedList<VCFRecord>(); } public LinkedList<VariantContext> reduceInit() { return new LinkedList<VariantContext>(); }
/** /**
@ -267,8 +266,8 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
* @param context the context for the given locus * @param context the context for the given locus
* @return 1 if the locus was successfully processed, 0 if otherwise * @return 1 if the locus was successfully processed, 0 if otherwise
*/ */
public LinkedList<VCFRecord> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public LinkedList<VariantContext> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
LinkedList<VCFRecord> result = new LinkedList<VCFRecord>(); LinkedList<VariantContext> result = new LinkedList<VariantContext>();
if ( tracker == null ) if ( tracker == null )
return result; return result;
@ -299,12 +298,12 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
if(multiThreadedMode) { if(multiThreadedMode) {
//keep results in memory, only writing them in onTraversalDone(..) after they have been merged via treeReduce(..) //keep results in memory, only writing them in onTraversalDone(..) after they have been merged via treeReduce(..)
for(VariantContext annotatedVC : annotatedVCs ) { for(VariantContext annotatedVC : annotatedVCs ) {
result.add(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase())); result.add(annotatedVC);
} }
} else { } else {
//write results to disk immediately //write results to disk immediately
for(VariantContext annotatedVC : annotatedVCs ) { for(VariantContext annotatedVC : annotatedVCs ) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase())); vcfWriter.add(annotatedVC, new byte[]{ref.getBase()});
} }
} }
@ -320,7 +319,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
* @param sum accumulator for the reduce. * @param sum accumulator for the reduce.
* @return the new number of loci processed. * @return the new number of loci processed.
*/ */
public LinkedList<VCFRecord> reduce(LinkedList<VCFRecord> value, LinkedList<VCFRecord> sum) { public LinkedList<VariantContext> reduce(LinkedList<VariantContext> value, LinkedList<VariantContext> sum) {
sum.addAll(value); sum.addAll(value);
return sum; return sum;
} }
@ -330,7 +329,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
/** /**
* Merge lists. * Merge lists.
*/ */
public LinkedList<VCFRecord> treeReduce(LinkedList<VCFRecord> lhs, LinkedList<VCFRecord> rhs) { public LinkedList<VariantContext> treeReduce(LinkedList<VariantContext> lhs, LinkedList<VariantContext> rhs) {
lhs.addAll(rhs); lhs.addAll(rhs);
return lhs; return lhs;
} }
@ -341,13 +340,13 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VCFRecord>, LinkedLis
/** /**
* Tell the user the number of loci processed and close out the new variants file. * Tell the user the number of loci processed and close out the new variants file.
* *
* @param result the number of loci seen. * @param totalOutputRecords all VCs seen.
*/ */
public void onTraversalDone(LinkedList<VCFRecord> totalOutputVCFRecords) { public void onTraversalDone(LinkedList<VariantContext> totalOutputRecords) {
if(multiThreadedMode) { if(multiThreadedMode) {
//finally write results to disk //finally write results to disk
for(VCFRecord vcfRecord : totalOutputVCFRecords ) { for(VariantContext vc : totalOutputRecords ) {
vcfWriter.addRecord(vcfRecord); vcfWriter.add(vc, vc.getReference().getBases());
} }
} }

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 = {"a1bd36fc69a3cdd3a08d951730b1d7be"}; String[] md5WithDashSArg = {"53c5d83d0d024482e0e69f9087df0a13"};
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 " +