org.broadinstitute.hellbender.tools.walkers.annotator

Class StrandBiasTest

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest

All Implemented Interfaces:

Annotation

Direct Known Subclasses:

AS_StrandBiasTest, FisherStrand, StrandOddsRatio

public abstract class StrandBiasTest
extends InfoFieldAnnotation

Class of tests to detect strand bias.

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	ARRAY_DIM
protected static int	ARRAY_SIZE

Constructor Summary

Constructors

Constructor and Description
StrandBiasTest()

Method Summary

Modifier and Type	Method and Description
java.util.Map<java.lang.String,java.lang.Object>	annotate(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods) Computes the annotation for the given variant and the likelihoods per read.
protected abstract java.util.Map<java.lang.String,java.lang.Object>	calculateAnnotationFromGTfield(htsjdk.variant.variantcontext.GenotypesContext genotypes)
protected abstract java.util.Map<java.lang.String,java.lang.Object>	calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods, htsjdk.variant.variantcontext.VariantContext vc)
static int[][]	decodeSBBS(int[] array) Helper function to turn the SB annotation array into a contingency table
static int[][]	getContingencyTable(AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods, htsjdk.variant.variantcontext.VariantContext vc, int minCount) Allocate and fill a 2x2 strand contingency table.
static int[][]	getContingencyTable(AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods, htsjdk.variant.variantcontext.VariantContext vc, int minCount, java.util.Collection<java.lang.String> samples) Allocate and fill a 2x2 strand contingency table.
static int[]	getStrandCounts(htsjdk.variant.variantcontext.Genotype g)
protected int[][]	getTableFromSamples(htsjdk.variant.variantcontext.GenotypesContext genotypes, int minCount) Create the contingency table by retrieving the per-sample strand bias annotation and adding them together
protected static boolean	passesMinimumThreshold(int[] data, int minCount) Does this strand data array pass the minimum threshold for inclusion?

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

getDescriptions

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

getKeyNames, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ARRAY_DIM

protected static final int ARRAY_DIM

See Also:

Constant Field Values

ARRAY_SIZE

protected static final int ARRAY_SIZE

See Also:

Constant Field Values

Constructor Detail

StrandBiasTest

public StrandBiasTest()

Method Detail

annotate

public java.util.Map<java.lang.String,java.lang.Object> annotate(ReferenceContext ref,
                                                                 htsjdk.variant.variantcontext.VariantContext vc,
                                                                 AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods)

Description copied from class: InfoFieldAnnotation

Computes the annotation for the given variant and the likelihoods per read. Returns a map from annotation keys to values (may be empty if no annotation is to be added).

Specified by:

annotate in class InfoFieldAnnotation

Parameters:

ref - Reference context, may be null

vc - Variant to be annotated. Not null.

likelihoods - likelihoods indexed by sample, allele, and read within sample

calculateAnnotationFromGTfield

protected abstract java.util.Map<java.lang.String,java.lang.Object> calculateAnnotationFromGTfield(htsjdk.variant.variantcontext.GenotypesContext genotypes)

calculateAnnotationFromLikelihoods

protected abstract java.util.Map<java.lang.String,java.lang.Object> calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods,
                                                                                                       htsjdk.variant.variantcontext.VariantContext vc)

getTableFromSamples

protected int[][] getTableFromSamples(htsjdk.variant.variantcontext.GenotypesContext genotypes,
                                      int minCount)

Create the contingency table by retrieving the per-sample strand bias annotation and adding them together

Parameters:

genotypes - the genotypes from which to pull out the per-sample strand bias annotation

minCount - minimum threshold for the sample strand bias counts for each ref and alt. If both ref and alt counts are above minCount the whole sample strand bias is added to the resulting table

Returns:

the table used for several strand bias tests, will be null if none of the genotypes contain the per-sample SB annotation

getStrandCounts

public static int[] getStrandCounts(htsjdk.variant.variantcontext.Genotype g)

getContingencyTable

public static int[][] getContingencyTable(AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods,
                                          htsjdk.variant.variantcontext.VariantContext vc,
                                          int minCount)

Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this: fw rc allele1 # # allele2 # #

Returns:

a 2x2 contingency table

getContingencyTable

public static int[][] getContingencyTable(AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods,
                                          htsjdk.variant.variantcontext.VariantContext vc,
                                          int minCount,
                                          java.util.Collection<java.lang.String> samples)

Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this: fw rc allele1 # # allele2 # #

Returns:

a 2x2 contingency table

passesMinimumThreshold

protected static boolean passesMinimumThreshold(int[] data,
                                                int minCount)

Does this strand data array pass the minimum threshold for inclusion?

Parameters:

data - the array

minCount - The minimum threshold of counts in the array

Returns:

true if it passes the minimum threshold, false otherwise

decodeSBBS

public static int[][] decodeSBBS(int[] array)

Helper function to turn the SB annotation array into a contingency table

Parameters:

array - the array used by the per-sample Strand Bias annotation

Returns:

the table used by the StrandBiasTest annotation