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

Removing dependencies in the annotations on extended events. Some refactoring involved in this.

This commit is contained in:
Eric Banks 2012-03-30 00:17:02 -04:00
parent c2e27729c7
commit 44ac49aa34
5 changed files with 38 additions and 91 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
View File

@ -41,7 +41,7 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
int depth = 0; int depth = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
depth += sample.getValue().hasBasePileup() ? sample.getValue().getBasePileup().depthOfCoverage() : sample.getValue().getExtendedEventPileup().depthOfCoverage(); depth += sample.getValue().hasBasePileup() ? sample.getValue().getBasePileup().depthOfCoverage() : 0;
Map<String, Object> map = new HashMap<String, Object>(); Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%d", depth)); map.put(getKeyNames().get(0), String.format("%d", depth));
return map; return map;

43
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -9,9 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.Genotype;
@ -44,9 +42,9 @@ import java.util.Map;
*/ */
public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation { public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation {
private static String REF_ALLELE = "REF"; private static final String REF_ALLELE = "REF";
private static String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) { public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() ) if ( g == null || !g.isCalled() )
@ -62,7 +60,8 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) { private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
if ( ! stratifiedContext.hasBasePileup() ) return null; if ( ! stratifiedContext.hasBasePileup() )
return null;
HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>(); HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
for ( Allele allele : vc.getAlleles() ) for ( Allele allele : vc.getAlleles() )
@ -87,17 +86,16 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
private Map<String,Object> annotateIndel(AlignmentContext stratifiedContext, VariantContext vc) { private Map<String,Object> annotateIndel(AlignmentContext stratifiedContext, VariantContext vc) {
if ( ! stratifiedContext.hasExtendedEventPileup() ) { if ( ! stratifiedContext.hasBasePileup() )
return null; return null;
}
ReadBackedExtendedEventPileup pileup = stratifiedContext.getExtendedEventPileup(); ReadBackedPileup pileup = stratifiedContext.getBasePileup();
if ( pileup == null ) if ( pileup == null )
return null; return null;
HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>(); final HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();
alleleCounts.put(REF_ALLELE,0); alleleCounts.put(REF_ALLELE, 0);
Allele refAllele = vc.getReference(); final Allele refAllele = vc.getReference();
for ( Allele allele : vc.getAlternateAlleles() ) { for ( Allele allele : vc.getAlternateAlleles() ) {
@ -108,33 +106,24 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
alleleCounts.put(getAlleleRepresentation(allele), 0); alleleCounts.put(getAlleleRepresentation(allele), 0);
} }
for ( ExtendedEventPileupElement e : pileup.toExtendedIterable() ) { for ( PileupElement p : pileup ) {
if ( e.isInsertion() ) { if ( p.isBeforeInsertion() ) {
final String b = e.getEventBases(); final String b = p.getEventBases();
if ( alleleCounts.containsKey(b) ) { if ( alleleCounts.containsKey(b) ) {
alleleCounts.put(b, alleleCounts.get(b)+1); alleleCounts.put(b, alleleCounts.get(b)+1);
} }
} else { } else if ( p.isBeforeDeletionStart() ) {
if ( e.isDeletion() ) { if ( p.getEventLength() == refAllele.length() ) {
if ( e.getEventLength() == refAllele.length() ) {
// this is indeed the deletion allele recorded in VC // this is indeed the deletion allele recorded in VC
final String b = DEL; final String b = DEL;
if ( alleleCounts.containsKey(b) ) { if ( alleleCounts.containsKey(b) ) {
alleleCounts.put(b, alleleCounts.get(b)+1); alleleCounts.put(b, alleleCounts.get(b)+1);
} }
} }
// else { } else if ( p.getRead().getAlignmentEnd() > vc.getStart() ) {
// System.out.print(" deletion of WRONG length found"); alleleCounts.put(REF_ALLELE, alleleCounts.get(REF_ALLELE)+1);
// }
}
else {
if ( e.getRead().getAlignmentEnd() <= vc.getStart() ) {
continue;
}
alleleCounts.put(REF_ALLELE,alleleCounts.get(REF_ALLELE)+1);
}
} }
} }

41
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -64,6 +64,9 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here
return null; return null;
if (!vc.isSNP() && !vc.isIndel() && !vc.isMixed())
return null;
final AlignmentContext context = AlignmentContextUtils.joinContexts(stratifiedContexts.values()); final AlignmentContext context = AlignmentContextUtils.joinContexts(stratifiedContexts.values());
final int contextWingSize = Math.min((ref.getWindow().size() - 1) / 2, MIN_CONTEXT_WING_SIZE); final int contextWingSize = Math.min((ref.getWindow().size() - 1) / 2, MIN_CONTEXT_WING_SIZE);
@ -71,41 +74,27 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final int locus = ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2; final int locus = ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2;
// Compute all haplotypes consistent with the current read pileup if ( !context.hasBasePileup() )
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup == null)
return null; return null;
final ReadBackedPileup pileup = context.getBasePileup();
// Compute all haplotypes consistent with the current read pileup
final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus, vc); final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus, vc);
final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage(); final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
if (haplotypes != null) { if (haplotypes != null) {
for (final Genotype genotype : vc.getGenotypes()) { for (final Genotype genotype : vc.getGenotypes()) {
final AlignmentContext thisContext = stratifiedContexts.get(genotype.getSampleName()); final AlignmentContext thisContext = stratifiedContexts.get(genotype.getSampleName());
if (thisContext != null) { if (thisContext != null && thisContext.hasBasePileup()) {
final ReadBackedPileup thisPileup; final ReadBackedPileup thisPileup = thisContext.getBasePileup();
if (thisContext.hasExtendedEventPileup()) if (vc.isSNP())
thisPileup = thisContext.getExtendedEventPileup(); scoreRA.add(scoreReadsAgainstHaplotypes(haplotypes, thisPileup, contextSize, locus)); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
else if (thisContext.hasBasePileup()) else if (vc.isIndel() || vc.isMixed()) {
thisPileup = thisContext.getBasePileup(); Double d = scoreIndelsAgainstHaplotypes(thisPileup);
else if (d == null)
thisPileup = null;
if (thisPileup != null) {
if (vc.isSNP())
scoreRA.add(scoreReadsAgainstHaplotypes(haplotypes, thisPileup, contextSize, locus)); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
else if (vc.isIndel() || vc.isMixed()) {
Double d = scoreIndelsAgainstHaplotypes(thisPileup);
if (d == null)
return null;
scoreRA.add(d); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
} else
return null; return null;
scoreRA.add(d); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
} }
} }
} }

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
View File

@ -62,12 +62,10 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
continue; continue;
} }
ReadBackedPileup pileup = null; if (!context.hasBasePileup())
if (context.hasExtendedEventPileup()) continue;
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
final ReadBackedPileup pileup = context.getBasePileup();
if (pileup == null) if (pileup == null)
continue; continue;

35
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.util.*; import java.util.*;
@ -168,20 +167,14 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
protected Boolean ALWAYS_APPEND_DBSNP_ID = false; protected Boolean ALWAYS_APPEND_DBSNP_ID = false;
public boolean alwaysAppendDbsnpId() { return ALWAYS_APPEND_DBSNP_ID; } public boolean alwaysAppendDbsnpId() { return ALWAYS_APPEND_DBSNP_ID; }
@Hidden
@Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
protected boolean indelsOnly = false;
@Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio") @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio")
public double minGenotypeQualityP = 0.0; public double minGenotypeQualityP = 0.0;
@Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp tracks that exactly match both reference and alternate alleles will be counted as concordant", required=false) @Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp tracks that exactly match both reference and alternate alleles will be counted as concordant", required=false)
private boolean requireStrictAlleleMatch = false; protected boolean requireStrictAlleleMatch = false;
private VariantAnnotatorEngine engine; private VariantAnnotatorEngine engine;
private Collection<VariantContext> indelBufferContext;
private void listAnnotationsAndExit() { private void listAnnotationsAndExit() {
System.out.println("\nStandard annotations in the list below are marked with a '*'."); System.out.println("\nStandard annotations in the list below are marked with a '*'.");
@ -261,10 +254,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
VCFHeader vcfHeader = new VCFHeader(hInfo, samples); VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader); vcfWriter.writeHeader(vcfHeader);
if ( indelsOnly ) {
indelBufferContext = null;
}
} }
public static boolean isUniqueHeaderLine(VCFHeaderLine line, Set<VCFHeaderLine> currentSet) { public static boolean isUniqueHeaderLine(VCFHeaderLine line, Set<VCFHeaderLine> currentSet) {
@ -294,13 +283,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
*/ */
public boolean includeReadsWithDeletionAtLoci() { return true; } public boolean includeReadsWithDeletionAtLoci() { return true; }
/**
* We want to see extended events if annotating indels
*
* @return true
*/
public boolean generateExtendedEvents() { return indelsOnly; }
/** /**
* For each site of interest, annotate based on the requested annotation types * For each site of interest, annotate based on the requested annotation types
* *
@ -334,19 +316,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
} }
} }
if ( ! indelsOnly ) { for ( VariantContext annotatedVC : annotatedVCs )
for ( VariantContext annotatedVC : annotatedVCs ) vcfWriter.add(annotatedVC);
vcfWriter.add(annotatedVC);
} else {
// check to see if the buffered context is different (in location) this context
if ( indelBufferContext != null && ! VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),indelBufferContext.iterator().next()).equals(VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),annotatedVCs.iterator().next())) ) {
for ( VariantContext annotatedVC : indelBufferContext )
vcfWriter.add(annotatedVC);
indelBufferContext = annotatedVCs;
} else {
indelBufferContext = annotatedVCs;
}
}
return 1; return 1;
} }