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Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this). 

Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-11 16:42:06 +00:00
parent dde93e743f
commit 8c28be5933
7 changed files with 25 additions and 13 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -383,6 +383,8 @@ public class VariantContextAdaptors {
result = VCFGenotypeRecord.getMissingFieldValue(key);
else if ( val instanceof Double )
result = String.format("%.2f", (Double)val);
else if ( val instanceof Boolean )
result = (Boolean)val ? "" : null; // empty string for true, null for false
else if ( val instanceof List ) {
List list = (List)val;
if ( list.size() == 0 )

8
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -73,6 +73,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
@Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
protected Boolean LIST = false;
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
protected String ASSUME_SINGLE_SAMPLE = null;
@Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
protected boolean indelsOnly = false;
@ -196,9 +199,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
Map<String, StratifiedAlignmentContext> stratifiedContexts;
if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
if ( ! context.hasExtendedEventPileup() ) {
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup(), ASSUME_SINGLE_SAMPLE, null);
} else {
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getExtendedEventPileup());
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getExtendedEventPileup(), ASSUME_SINGLE_SAMPLE, null);
}
if ( stratifiedContexts != null ) {
annotatedVCs = engine.annotateContext(tracker, ref, stratifiedContexts, vc);
@ -206,7 +209,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
}
if ( ! indelsOnly ) {
if ( variant instanceof VCFRecord ) {
for(VariantContext annotatedVC : annotatedVCs ) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase()));

12
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -186,11 +186,11 @@ public class VariantAnnotatorEngine {
for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations )
descriptions.addAll(annotation.getDescriptions());
if ( annotateDbsnp )
descriptions.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP Membership"));
descriptions.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Flag, "dbSNP Membership"));
if ( annotateHapmap2 )
descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP2_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 2 Membership"));
descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP2_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Flag, "Hapmap 2 Membership"));
if ( annotateHapmap3 )
descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP3_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 3 Membership"));
descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP3_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Flag, "Hapmap 3 Membership"));
return descriptions;
}
@ -202,7 +202,7 @@ public class VariantAnnotatorEngine {
// annotate dbsnp occurrence
if ( annotateDbsnp ) {
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 ? false : true);
// annotate dbsnp id if available and not already there
if ( dbsnp != null && (!vc.hasAttribute("ID") || vc.getAttribute("ID").equals(VCFRecord.EMPTY_ID_FIELD)) )
infoAnnotations.put("ID", dbsnp.getRsID());
@ -210,12 +210,12 @@ public class VariantAnnotatorEngine {
if ( annotateHapmap2 ) {
List<Object> hapmap2 = tracker.getReferenceMetaData("hapmap2");
infoAnnotations.put(VCFRecord.HAPMAP2_KEY, hapmap2.size() == 0 ? "0" : "1");
infoAnnotations.put(VCFRecord.HAPMAP2_KEY, hapmap2.size() == 0 ? false : true);
}
if ( annotateHapmap3 ) {
List<Object> hapmap3 = tracker.getReferenceMetaData("hapmap3");
infoAnnotations.put(VCFRecord.HAPMAP3_KEY, hapmap3.size() == 0 ? "0" : "1");
infoAnnotations.put(VCFRecord.HAPMAP3_KEY, hapmap3.size() == 0 ? false : true);
}
//Process the info field

12
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -113,8 +113,16 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -L 1:10,000,000-10,050,000", 1,
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("07af9983127c62e96accc03db2fb523e"));
executeTest("test file doesn't have annotations, not passing it any reads", spec);
executeTest("not passing it any reads", spec);
}
@Test
public void testDBTag() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("286887826ab99bb2864f7f4db195e59e"));
executeTest("getting DB tag", spec);
}
}

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 = {"fb6f52b72610a4f6bcf4c130ec14705a"};
String[] md5WithDashSArg = {"35dffbdb99dbf480f4bc5169219bcfc1"};
WalkerTestSpec specWithSArg = new WalkerTestSpec(
"-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 " +

BIN
settings/repository/org.broad/tribble-102.jar → settings/repository/org.broad/tribble-103.jar
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2
settings/repository/org.broad/tribble-102.xml → settings/repository/org.broad/tribble-103.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="102" status="integration" publication="201006101154200" />
<info organisation="org.broad" module="tribble" revision="103" status="integration" publication="201006101154200" />
</ivy-module>