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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-08-10 13:42:37 -04:00
parent 749c8bfbcd 0497170bc9
commit 8d14d32a62
34 changed files with 151 additions and 54 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -44,7 +46,7 @@ import java.util.Map;
public class AlleleBalance extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -17,7 +19,7 @@ import java.util.*;
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
Double ratio = annotateSNP(stratifiedContext, vc, g);
if (ratio == null)
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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@ -31,6 +31,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -48,7 +50,7 @@ import java.util.Map;
public class BaseCounts extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -50,7 +52,7 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( ! vc.hasGenotypes() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,7 +20,7 @@ import java.util.Map;
public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -28,7 +30,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
private static 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, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import cern.jet.math.Arithmetic;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -46,7 +48,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
private static final String FS = "FS";
private static final double MIN_PVALUE = 1E-320;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( ! vc.isVariant() || vc.isFiltered() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,7 +20,7 @@ import java.util.Map;
public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
double content = computeGCContent(ref);
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", content));

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -27,7 +29,7 @@ public class GLstats extends InfoFieldAnnotation implements StandardAnnotation {
private static final int MIN_SAMPLES = 10;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
final Map<String, Genotype> genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() < MIN_SAMPLES )

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import net.sf.samtools.SAMRecord;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -54,7 +56,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;
private final static char REGEXP_WILDCARD = '.';
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if (stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
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@ -1,6 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -24,7 +26,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress
private static final int MIN_GENOTYPE_QUALITY = 10;
private static final int MIN_NEG_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
final Map<String, Genotype> genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() < MIN_SAMPLES )

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -20,7 +22,7 @@ public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnot
private boolean ANNOTATE_INDELS = true;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.isBiallelic() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -21,7 +23,7 @@ import java.util.*;
*/
public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
int run;
if (vc.isMixed()) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,7 +20,7 @@ import java.util.Map;
public class LowMQ extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -20,7 +22,7 @@ import java.util.Map;
public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -50,8 +52,8 @@ import java.util.Map;
* To change this template use File | Settings | File Templates.
*/
public class MappingQualityZeroBySample extends GenotypeAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
AlignmentContext context, VariantContext vc, Genotype g) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings,
ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -20,7 +22,7 @@ import java.util.Map;
public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -22,7 +24,7 @@ import java.util.Map;
*/
public class NBaseCount extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,7 +20,7 @@ import java.util.Map;
public class QualByDepth extends AnnotationByDepth implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -22,7 +24,7 @@ import java.util.Map;
public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -25,7 +27,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
static final double INDEL_LIKELIHOOD_THRESH = 0.1;
static final boolean DEBUG = false;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -58,7 +60,7 @@ public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
private static 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, ReferenceContext ref,
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref,
AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,7 +20,7 @@ import java.util.Map;
public class SBByDepth extends AnnotationByDepth {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -43,7 +45,7 @@ import java.util.Map;
public class SampleList extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( vc.isMonomorphic() || !vc.hasGenotypes() )
return null;

22
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -69,8 +70,11 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
public static final String CODON_NUM_KEY = "CODON_NUM";
public static final String CDS_SIZE_KEY = "CDS_SIZE";
public Map<String, Object> annotate ( RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
List<Feature> features = tracker.getValues(Feature.class);
public static final String SNPEFF_ROD_NAME = "snpEffFile";
public Map<String, Object> annotate ( RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
RodBinding<SnpEffFeature> snpEffRodBinding = (RodBinding<SnpEffFeature>)rodBindings.get(SNPEFF_ROD_NAME);
List<SnpEffFeature> features = tracker.getValues(snpEffRodBinding);
// Add only annotations for one of the most biologically-significant effects as defined in
// the SnpEffConstants class:
@ -83,18 +87,14 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
return generateAnnotations(mostSignificantEffect);
}
private SnpEffFeature getMostSignificantEffect ( List<Feature> features ) {
private SnpEffFeature getMostSignificantEffect ( List<SnpEffFeature> snpEffFeatures ) {
SnpEffFeature mostSignificantEffect = null;
for ( Feature feature : features ) {
if ( feature instanceof SnpEffFeature ) {
SnpEffFeature snpEffFeature = (SnpEffFeature)feature;
for ( SnpEffFeature snpEffFeature : snpEffFeatures ) {
if ( mostSignificantEffect == null ||
snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
if ( mostSignificantEffect == null ||
snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
mostSignificantEffect = snpEffFeature;
}
mostSignificantEffect = snpEffFeature;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
View File

@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,7 +20,7 @@ import java.util.Map;
public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
View File

@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -29,7 +31,7 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi
private String n454 ="Num454";
private String nSolid = "NumSOLiD";
private String nOther = "NumOther";
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

24
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
@ -59,8 +60,14 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/**
* A SnpEff output file from which to add annotations.
*
* The INFO field will be annotated with information on the most biologically-significant effect
* listed in the SnpEff output file for each variant.
*/
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
public RodBinding<SnpEffFeature> snpEffFile = RodBinding.makeUnbound(SnpEffFeature.class);
/**
* A dbSNP VCF file from which to annotate.
@ -115,6 +122,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
private Collection<VariantContext> indelBufferContext;
private Map<String, RodBinding<? extends Feature>> rodBindings = new HashMap<String, RodBinding<? extends Feature>>();
private void listAnnotationsAndExit() {
List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
@ -157,10 +166,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
}
initializeRodBindingMap();
if ( USE_ALL_ANNOTATIONS )
engine = new VariantAnnotatorEngine(getToolkit());
engine = new VariantAnnotatorEngine(getToolkit(), rodBindings);
else
engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse);
engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse, rodBindings);
engine.initializeExpressions(expressionsToUse);
// setup the header fields
@ -180,6 +191,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
}
}
private void initializeRodBindingMap() {
rodBindings.put(variantCollection.variants.getName(), variantCollection.variants);
rodBindings.put(snpEffFile.getName(), snpEffFile);
rodBindings.put(dbsnp.dbsnp.getName(), dbsnp.dbsnp);
rodBindings.put(comps.getName(), comps);
}
public static boolean isUniqueHeaderLine(VCFHeaderLine line, Set<VCFHeaderLine> currentSet) {
if ( !(line instanceof VCFCompoundHeaderLine) )
return true;

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -55,7 +56,7 @@ public class VariantAnnotatorEngine {
private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
private HashMap<String, String> dbAnnotations = new HashMap<String, String>();
private Map<String, RodBinding<? extends Feature>> rodBindings;
private static class VAExpression {
public String fullName, bindingName, fieldName;
@ -72,16 +73,18 @@ public class VariantAnnotatorEngine {
}
// use this constructor if you want all possible annotations
public VariantAnnotatorEngine(GenomeAnalysisEngine engine) {
public VariantAnnotatorEngine(GenomeAnalysisEngine engine, Map<String, RodBinding<? extends Feature>> rodBindings) {
requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
requestedGenotypeAnnotations = AnnotationInterfaceManager.createAllGenotypeAnnotations();
initializeDBs(engine);
this.rodBindings = rodBindings;
}
// use this constructor if you want to select specific annotations (and/or interfaces)
public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse) {
public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse, Map<String, RodBinding<? extends Feature>> rodBindings) {
initializeAnnotations(annotationGroupsToUse, annotationsToUse);
initializeDBs(engine);
this.rodBindings = rodBindings;
}
// select specific expressions to use
@ -137,7 +140,7 @@ public class VariantAnnotatorEngine {
// go through all the requested info annotationTypes
for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
Map<String, Object> annotationsFromCurrentType = annotationType.annotate(tracker, ref, stratifiedContexts, vc);
Map<String, Object> annotationsFromCurrentType = annotationType.annotate(tracker, rodBindings, ref, stratifiedContexts, vc);
if ( annotationsFromCurrentType != null )
infoAnnotations.putAll(annotationsFromCurrentType);
}
@ -202,7 +205,7 @@ public class VariantAnnotatorEngine {
Map<String, Object> genotypeAnnotations = new HashMap<String, Object>(genotype.getAttributes());
for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
Map<String, Object> result = annotation.annotate(tracker, ref, context, vc, genotype);
Map<String, Object> result = annotation.annotate(tracker, rodBindings, ref, context, vc, genotype);
if ( result != null )
genotypeAnnotations.putAll(result);
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
View File

@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -13,7 +15,8 @@ import java.util.Map;
public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts/genotype split by sample
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings,
ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
// return the descriptions used for the VCF FORMAT meta field
public abstract List<VCFFormatHeaderLine> getDescriptions();

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
View File

@ -1,11 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
@ -13,7 +13,8 @@ import java.util.Map;
public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts split by sample
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings,
ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
// return the descriptions used for the VCF INFO meta field
public abstract List<VCFInfoHeaderLine> getDescriptions();

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -25,9 +25,11 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -138,7 +140,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
if ( verboseWriter != null )
verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tAFposterior\tNormalizedPosterior");
annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse);
// TODO: Fill in the final argument with actual RodBinding map
annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse, new HashMap<String, RodBinding<? extends Feature>>());
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
// initialize the header

19
public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
View File

@ -27,11 +27,16 @@ package org.broadinstitute.sting.utils.codecs.snpEff;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.LineReader;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType;
import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType;
import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
/**
@ -68,7 +73,7 @@ import java.io.IOException;
*
* @author David Roazen
*/
public class SnpEffCodec implements FeatureCodec {
public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
public static final int EXPECTED_NUMBER_OF_FIELDS = 23;
public static final String FIELD_DELIMITER_PATTERN = "\\t";
@ -255,4 +260,16 @@ public class SnpEffCodec implements FeatureCodec {
}
}
}
public boolean canDecode ( final File potentialInput ) {
try {
LineReader reader = new AsciiLineReader(new FileInputStream(potentialInput));
readHeader(reader);
}
catch ( Exception e ) {
return false;
}
return true;
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -129,8 +129,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testSnpEffAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant:VCF " +
validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation +
"-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant " +
validationDataLocation + "1000G.exomes.vcf --snpEffFile " + validationDataLocation +
"snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
1,
Arrays.asList("c08648a078368c80530bff004b3157f1")