Merge pull request #708 from broadinstitute/ldg_SBannotationWarnings
Refactor StrandBiasTest (using template method) and add warnings for whe...
This commit is contained in:
Eric Banks
commit
78c2da1fef
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@ -47,6 +47,8 @@
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package org.broadinstitute.gatk.tools.walkers.annotator;
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import cern.jet.math.Arithmetic;
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import htsjdk.variant.variantcontext.Genotype;
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import htsjdk.variant.variantcontext.GenotypesContext;
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import org.apache.log4j.Logger;
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import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
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import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
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@ -87,42 +89,34 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation,
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private static final int MIN_QUAL_FOR_FILTERED_TEST = 17;
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private static final int MIN_COUNT = 2;
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public Map<String, Object> annotate(final RefMetaDataTracker tracker,
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final AnnotatorCompatible walker,
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final ReferenceContext ref,
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final Map<String, AlignmentContext> stratifiedContexts,
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final VariantContext vc,
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final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
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if ( !vc.isVariant() )
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return null;
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if ( vc.hasGenotypes() ) {
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final int[][] tableFromPerSampleAnnotations = getTableFromSamples( vc.getGenotypes(), MIN_COUNT );
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if ( tableFromPerSampleAnnotations != null ) {
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return pValueForBestTable(tableFromPerSampleAnnotations, null);
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}
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}
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if (vc.isSNP() && stratifiedContexts != null) {
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final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1, MIN_COUNT);
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final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), MIN_QUAL_FOR_FILTERED_TEST, MIN_COUNT);
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printTable("unfiltered", tableNoFiltering);
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printTable("filtered", tableFiltering);
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return pValueForBestTable(tableFiltering, tableNoFiltering);
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}
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else if (stratifiedPerReadAlleleLikelihoodMap != null) {
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// either SNP with no alignment context, or indels: per-read likelihood map needed
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final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT);
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//logger.info("VC " + vc);
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//printTable(table, 0.0);
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return pValueForBestTable(table, null);
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}
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else
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// for non-snp variants, we need per-read likelihoods.
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// for snps, we can get same result from simple pileup
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return null;
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@Override
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protected Map<String, Object> calculateAnnotationFromGTfield(final GenotypesContext genotypes){
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final int[][] tableFromPerSampleAnnotations = getTableFromSamples( genotypes, MIN_COUNT );
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return ( tableFromPerSampleAnnotations != null )? pValueForBestTable(tableFromPerSampleAnnotations, null) : null;
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}
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@Override
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protected Map<String, Object> calculateAnnotationFromStratifiedContexts(final Map<String, AlignmentContext> stratifiedContexts,
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final VariantContext vc){
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final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1, MIN_COUNT);
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final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), MIN_QUAL_FOR_FILTERED_TEST, MIN_COUNT);
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printTable("unfiltered", tableNoFiltering);
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printTable("filtered", tableFiltering);
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return pValueForBestTable(tableFiltering, tableNoFiltering);
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}
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@Override
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protected Map<String, Object> calculateAnnotationFromLikelihoodMap(final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
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final VariantContext vc){
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// either SNP with no alignment context, or indels: per-read likelihood map needed
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final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT);
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//logger.info("VC " + vc);
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//printTable(table, 0.0);
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return pValueForBestTable(table, null);
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}
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/**
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* Create an annotation for the highest (i.e., least significant) p-value of table1 and table2
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*
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@ -48,7 +48,15 @@ package org.broadinstitute.gatk.tools.walkers.annotator;
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import htsjdk.variant.variantcontext.Allele;
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import htsjdk.variant.variantcontext.VariantContext;
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import htsjdk.variant.vcf.VCFFormatHeaderLine;
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import htsjdk.variant.vcf.VCFHeaderLine;
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import htsjdk.variant.vcf.VCFInfoHeaderLine;
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import org.apache.log4j.Logger;
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import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
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import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
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import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
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import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
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import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
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import htsjdk.variant.variantcontext.Genotype;
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import htsjdk.variant.variantcontext.GenotypesContext;
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@ -64,6 +72,83 @@ import java.util.*;
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* Class of tests to detect strand bias.
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*/
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public abstract class StrandBiasTest extends InfoFieldAnnotation {
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private final static Logger logger = Logger.getLogger(StrandBiasTest.class);
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@Override
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public void initialize(final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set<VCFHeaderLine> headerLines) {
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boolean hasSBBSannotation = false;
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for ( final VCFHeaderLine line : headerLines) {
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if ( line instanceof VCFFormatHeaderLine) {
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final VCFFormatHeaderLine formatline = (VCFFormatHeaderLine)line;
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if ( formatline.getID().equals(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME) ) {
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hasSBBSannotation = true;
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break;
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}
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}
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}
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if (hasSBBSannotation) {
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logger.info("StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample " +
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"values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.");
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return;
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}
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boolean hasReads = toolkit.getReadsDataSource().getReaderIDs().size() > 0;
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if (hasReads) {
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logger.info("SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.");
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return;
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}
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logger.info(new String("No StrandBiasBySample annotation or read data was found. Strand bias annotations will not be output."));
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}
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@Override
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//template method for calculating strand bias annotations using the three different methods
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public Map<String, Object> annotate(final RefMetaDataTracker tracker,
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final AnnotatorCompatible walker,
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final ReferenceContext ref,
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final Map<String,AlignmentContext> stratifiedContexts,
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final VariantContext vc,
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final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
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if ( !vc.isVariant() )
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return null;
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if ( vc.hasGenotypes() ) {
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boolean hasSB = false;
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for (final Genotype g : vc.getGenotypes()) {
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if (g.hasAnyAttribute(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME)) {
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hasSB = true;
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break;
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}
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}
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if (hasSB)
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return calculateAnnotationFromGTfield(vc.getGenotypes());
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}
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//stratifiedContexts can come come from VariantAnnotator, but will be size 0 if no reads were provided
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if (vc.isSNP() && stratifiedContexts != null && stratifiedContexts.size() > 0) {
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return calculateAnnotationFromStratifiedContexts(stratifiedContexts, vc);
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}
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//stratifiedPerReadAllelelikelihoodMap can come from HaplotypeCaller call to VariantAnnotatorEngine
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else if (stratifiedPerReadAlleleLikelihoodMap != null) {
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return calculateAnnotationFromLikelihoodMap(stratifiedPerReadAlleleLikelihoodMap, vc);
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}
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else
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// for non-snp variants, we need per-read likelihoods.
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// for snps, we can get same result from simple pileup
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return null;
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}
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protected abstract Map<String, Object> calculateAnnotationFromGTfield(final GenotypesContext genotypes);
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protected abstract Map<String, Object> calculateAnnotationFromStratifiedContexts(final Map<String, AlignmentContext> stratifiedContexts,
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final VariantContext vc);
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protected abstract Map<String, Object> calculateAnnotationFromLikelihoodMap(final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
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final VariantContext vc);
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/**
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* Create the contingency table by retrieving the per-sample strand bias annotation and adding them together
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* @param genotypes the genotypes from which to pull out the per-sample strand bias annotation
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@ -108,9 +193,9 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation {
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final int minCount ) {
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int[][] table = new int[2][2];
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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for (final Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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final int[] myTable = new int[4];
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for (PileupElement p : sample.getValue().getBasePileup()) {
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for (final PileupElement p : sample.getValue().getBasePileup()) {
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if ( ! isUsableBase(p) ) // ignore deletions and bad MQ
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continue;
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@ -46,6 +46,8 @@
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package org.broadinstitute.gatk.tools.walkers.annotator;
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import htsjdk.variant.variantcontext.Genotype;
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import htsjdk.variant.variantcontext.GenotypesContext;
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import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
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import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
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import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
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@ -79,38 +81,30 @@ public class StrandOddsRatio extends StrandBiasTest implements ActiveRegionBased
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private static final String SOR = "SOR";
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@Override
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public Map<String, Object> annotate(final RefMetaDataTracker tracker,
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final AnnotatorCompatible walker,
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final ReferenceContext ref,
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final Map<String,AlignmentContext> stratifiedContexts,
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final VariantContext vc,
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final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
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if ( !vc.isVariant() )
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return null;
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if ( vc.hasGenotypes() ) {
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final int[][] tableFromPerSampleAnnotations = getTableFromSamples( vc.getGenotypes(), MIN_COUNT );
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if ( tableFromPerSampleAnnotations != null ) {
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final double ratio = calculateSOR(tableFromPerSampleAnnotations);
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return annotationForOneTable(ratio);
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}
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}
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if (vc.isSNP() && stratifiedContexts != null) {
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final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1, MIN_COUNT);
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final double ratio = calculateSOR(tableNoFiltering);
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protected Map<String, Object> calculateAnnotationFromGTfield(GenotypesContext genotypes){
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final int[][] tableFromPerSampleAnnotations = getTableFromSamples( genotypes, MIN_COUNT );
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if ( tableFromPerSampleAnnotations != null ) {
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final double ratio = calculateSOR(tableFromPerSampleAnnotations);
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return annotationForOneTable(ratio);
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}
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else if (stratifiedPerReadAlleleLikelihoodMap != null) {
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// either SNP with no alignment context, or indels: per-read likelihood map needed
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final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT);
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final double ratio = calculateSOR(table);
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return annotationForOneTable(ratio);
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}
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else
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// for non-snp variants, we need per-read likelihoods.
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// for snps, we can get same result from simple pileup
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return null;
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return null;
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}
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@Override
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protected Map<String, Object> calculateAnnotationFromStratifiedContexts(Map<String, AlignmentContext> stratifiedContexts,
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final VariantContext vc){
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final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1, MIN_COUNT);
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final double ratio = calculateSOR(tableNoFiltering);
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return annotationForOneTable(ratio);
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}
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@Override
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protected Map<String, Object> calculateAnnotationFromLikelihoodMap(Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
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final VariantContext vc){
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// either SNP with no alignment context, or indels: per-read likelihood map needed
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final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT);
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final double ratio = calculateSOR(table);
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return annotationForOneTable(ratio);
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}
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/**
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@ -155,7 +155,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoReads() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("1c423b7730b9805e7b885ece924286e0"));
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Arrays.asList("e86d04320dc9a597c1f58ad4b03b33c3"));
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executeTest("not passing it any reads", spec);
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}
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@ -163,7 +163,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("54d7d5bb9404652857adf5e50d995f30"));
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Arrays.asList("bcccbe1c8572d98fa73d824d80ea0a05"));
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executeTest("getting DB tag with dbSNP", spec);
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}
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@ -171,7 +171,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testMultipleIdsWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
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Arrays.asList("5fe63e511061ed4f91d938e72e7e3c39"));
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Arrays.asList("e9d82ed45249833803aad9ebf2a686c2"));
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executeTest("adding multiple IDs with dbSNP", spec);
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}
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@ -179,7 +179,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithHapMap() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("cc7184263975595a6e2473d153227146"));
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Arrays.asList("2ff3d4bdaa9e0cc2688b26fed601c184"));
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executeTest("getting DB tag with HM3", spec);
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}
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@ -187,7 +187,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithTwoComps() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("6afbf05090ae139f53467cf6e0e71cf4"));
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Arrays.asList("dbffbec98dc60850a6bde11540e8040c"));
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executeTest("getting DB tag with 2 comps", spec);
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}
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@ -203,7 +203,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testUsingExpression() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("2b0e8cdfd691779befc5ac123d1a1887"));
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Arrays.asList("fb00c3b512926f8036829e53fd7f369a"));
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executeTest("using expression", spec);
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}
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@ -211,7 +211,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testUsingExpressionWithID() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("3de1d1998203518098ffae233f3e2352"));
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Arrays.asList("915f72e6cbeb7a77cd2746b4a99a6d64"));
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executeTest("using expression with ID", spec);
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}
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