org.broadinstitute.hellbender.utils.pairhmm

Class PairHMMModel

java.lang.Object

org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel

public final class PairHMMModel
extends java.lang.Object

Helper class that implement calculations required to implement the PairHMM Finite State Automation (FSA) model.

Field Summary

Fields

Modifier and Type	Field and Description
static int	deletionToDeletion Position in the transition probability array for the Deletion-to-Deletion transition.
static int	indelToMatch Position in the transition probability array for the Indel-to-Match transition.
static int	insertionToInsertion Position in the transition probability array for the Insertion-to-Insertion transition.
static int	matchToDeletion Position in the transition probability array for the Match-to-Deletion transition.
static int	matchToInsertion Position in the transition probability array for the Match-to-Insertion transition.
static int	matchToMatch Position in the transition probability array for the Match-to-Match transition.
static int	TRANS_PROB_ARRAY_LENGTH Length of the standard transition probability array.

Method Summary

Modifier and Type	Method and Description
static double[][]	createTransitionMatrix(int maxReadLength) Creates a transition probability matrix large enough to work with sequences of a particular length.
static double	matchToMatchProb(byte insQual, byte delQual) Returns the probability that neither of two event takes place.
static double	matchToMatchProb(int insQual, int delQual) Returns the probability that neither of two events, insertion and deletion, takes place.
static double	matchToMatchProbLog10(byte insQual, byte delQual) Returns the log10 probability that neither of two events, insertion and deletion, takes place.
static double	matchToMatchProbLog10(int insQual, int delQual) Returns the log-probability that neither of two events takes place.
static double[][]	qualToTransProbs(byte[] insQuals, byte[] delQuals, byte[] gcps) Returns a matrix with the transition probabilities for a number of bases.
static double[]	qualToTransProbs(byte insQual, byte delQual, byte gcp) Returns a transition probability array given the different quality scores affecting a read site.
static void	qualToTransProbs(double[][] dest, byte[] insQuals, byte[] delQuals, byte[] gcps) Fills ax matrix with the transition probabilities for a number of bases.
static void	qualToTransProbs(double[] dest, byte insQual, byte delQual, byte gcp) Fills a transition probability array given the different quality scores affecting a read site
static double[][]	qualToTransProbsLog10(byte[] insQuals, byte[] delQuals, byte[] gcps) Returns a matrix with the log10 transition probabilities for a number of bases.
static double[]	qualToTransProbsLog10(byte insQual, byte delQual, byte gcp) Returns a transition log10 probability array given the different quality scores affecting a read site.
static void	qualToTransProbsLog10(double[][] dest, byte[] insQuals, byte[] delQuals, byte[] gcps) Fills a matrix with the log10 transition probabilities for a number of bases.
static void	qualToTransProbsLog10(double[] dest, byte insQual, byte delQual, byte gcp) Fills a transition log10-probability array given the different quality scores affecting a read site.

Methods inherited from class java.lang.Object

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

Field Detail

TRANS_PROB_ARRAY_LENGTH

public static final int TRANS_PROB_ARRAY_LENGTH

Length of the standard transition probability array.

See Also:

Constant Field Values

matchToMatch

public static final int matchToMatch

Position in the transition probability array for the Match-to-Match transition.

See Also:

Constant Field Values

indelToMatch

public static final int indelToMatch

Position in the transition probability array for the Indel-to-Match transition.

See Also:

Constant Field Values

matchToInsertion

public static final int matchToInsertion

Position in the transition probability array for the Match-to-Insertion transition.

See Also:

Constant Field Values

insertionToInsertion

public static final int insertionToInsertion

Position in the transition probability array for the Insertion-to-Insertion transition.

See Also:

Constant Field Values

matchToDeletion

public static final int matchToDeletion

Position in the transition probability array for the Match-to-Deletion transition.

See Also:

Constant Field Values

deletionToDeletion

public static final int deletionToDeletion

Position in the transition probability array for the Deletion-to-Deletion transition.

See Also:

Constant Field Values

Method Detail

qualToTransProbs

public static void qualToTransProbs(double[] dest,
                                    byte insQual,
                                    byte delQual,
                                    byte gcp)

Fills a transition probability array given the different quality scores affecting a read site

Parameters:

insQual - the insertion quality score as a byte.

delQual - the deletion quality score as a byte.

gcp - the gap-continuation-penalty score as a byte.

Throws:

java.lang.NullPointerException - if dest is null.

java.lang.ArrayIndexOutOfBoundsException - if dest is not large enough.

java.lang.IllegalArgumentException - if insQual, delQual or gcp is less than negative.

qualToTransProbs

public static double[] qualToTransProbs(byte insQual,
                                        byte delQual,
                                        byte gcp)

Returns a transition probability array given the different quality scores affecting a read site.

Parameters:

insQual - the insertion quality score as a byte.

delQual - the deletion quality score as a byte.

gcp - the gap-continuation-penalty score as a byte.

Returns:

never null. An array of length TRANS_PROB_ARRAY_LENGTH.

Throws:

java.lang.NullPointerException - if dest is null.

java.lang.ArrayIndexOutOfBoundsException - if dest is not large enough.

java.lang.IllegalArgumentException - if insQual, delQual or gcp is less than negative.

qualToTransProbs

public static void qualToTransProbs(double[][] dest,
                                    byte[] insQuals,
                                    byte[] delQuals,
                                    byte[] gcps)

Fills ax matrix with the transition probabilities for a number of bases.

The first dimension of the matrix correspond to the different bases where the first one is stored in position 1. Thus the position 0 is left empty and the length of the resulting matrix is actually insQual.length + 1.

Each entry is the transition probability array for that base with a length of TRANS_PROB_ARRAY_LENGTH.

Parameters:

dest - the matrix to update

insQuals - insertion qualities.

delQuals - deletion qualities.

gcps - gap-continuation penalty qualities.

Throws:

java.lang.NullPointerException - if any of the input arrays, matrices is null or any entry in dest is null.

java.lang.IllegalArgumentException - if IllegalArgumentException if the input array don't have the same length.

java.lang.ArrayIndexOutOfBoundsException - if dest or any of its elements is not large enough to contain the transition matrix.

qualToTransProbs

public static double[][] qualToTransProbs(byte[] insQuals,
                                          byte[] delQuals,
                                          byte[] gcps)

Returns a matrix with the transition probabilities for a number of bases.

The first dimension of the matrix correspond to the different bases where the first one is stored in position 1. Thus the position 0 is left empty and the length of the resulting matrix is actually insQual.length + 1.

Each entry is the transition probability array for that base with a length of TRANS_PROB_ARRAY_LENGTH.

Parameters:

insQuals - insertion qualities.

delQuals - deletion qualities.

gcps - gap-continuation penalty qualities.

Returns:

never null, an matrix of the dimensions explained above.

Throws:

java.lang.NullPointerException - if any of the input arrays is null.

java.lang.IllegalArgumentException - if IllegalArgumentException if the input array don't have the same length.

qualToTransProbsLog10

public static void qualToTransProbsLog10(double[] dest,
                                         byte insQual,
                                         byte delQual,
                                         byte gcp)

Fills a transition log10-probability array given the different quality scores affecting a read site.

Parameters:

insQual - the insertion quality score as a byte.

delQual - the deletion quality score as a byte.

gcp - the gap-continuation-penalty score as a byte.

Throws:

java.lang.NullPointerException - if dest is null.

java.lang.ArrayIndexOutOfBoundsException - if dest is not large enough.

java.lang.IllegalArgumentException - if insQual, delQual or gcp is less than negative.

qualToTransProbsLog10

public static double[] qualToTransProbsLog10(byte insQual,
                                             byte delQual,
                                             byte gcp)

Returns a transition log10 probability array given the different quality scores affecting a read site.

Parameters:

insQual - the insertion quality score as a byte.

delQual - the deletion quality score as a byte.

gcp - the gap-continuation-penalty score as a byte.

Returns:

never null. An array of length TRANS_PROB_ARRAY_LENGTH.

Throws:

java.lang.NullPointerException - if dest is null.

java.lang.ArrayIndexOutOfBoundsException - if dest is not large enough.

java.lang.IllegalArgumentException - if insQual, delQual or gcp is less than negative.

qualToTransProbsLog10

public static void qualToTransProbsLog10(double[][] dest,
                                         byte[] insQuals,
                                         byte[] delQuals,
                                         byte[] gcps)

Fills a matrix with the log10 transition probabilities for a number of bases.

The first dimension of the matrix correspond to the different bases where the first one is stored in position 1. Thus the position 0 is left empty and the length of the resulting matrix is actually insQual.length + 1.

Each entry is the transition probability array for that base with a length of TRANS_PROB_ARRAY_LENGTH.

Parameters:

insQuals - insertion qualities.

delQuals - deletion qualities.

gcps - gap-continuation penalty qualities.

Throws:

java.lang.NullPointerException - if any of the input arrays, matrices is null or any entry in dest is null.

java.lang.IllegalArgumentException - if IllegalArgumentException if the input array don't have the same length.

java.lang.ArrayIndexOutOfBoundsException - if dest or any of its elements is not large enough to contain the transition matrix.

qualToTransProbsLog10

public static double[][] qualToTransProbsLog10(byte[] insQuals,
                                               byte[] delQuals,
                                               byte[] gcps)

Returns a matrix with the log10 transition probabilities for a number of bases.

The first dimension of the matrix correspond to the different bases where the first one is stored in position 1. Thus the position 0 is left empty and the length of the resulting matrix is actually insQual.length + 1.

Each entry is the transition probability array for that base with a length of TRANS_PROB_ARRAY_LENGTH.

Parameters:

insQuals - insertion qualities.

delQuals - deletion qualities.

gcps - gap-continuation penalty qualities.

Returns:

never null, an matrix of the dimensions explained above.

Throws:

java.lang.NullPointerException - if any of the input arrays is null.

java.lang.IllegalArgumentException - if IllegalArgumentException if the input array don't have the same length.

createTransitionMatrix

public static double[][] createTransitionMatrix(int maxReadLength)

Creates a transition probability matrix large enough to work with sequences of a particular length.

Parameters:

maxReadLength - the maximum read length for the transition matrix.

Returns:

never null. A matrix of maxReadLength + 1 by TRANS_PROB_ARRAY_LENGTH positions.

matchToMatchProb

public static double matchToMatchProb(byte insQual,
                                      byte delQual)

Returns the probability that neither of two event takes place.

We assume that both event never occur together and that delQual is the conditional probability (qual. encoded) of the second event, given the first event didn't took place. So that the probability of no event is:
We assume that both event never occur together so that the probability of no event is:
1 - ProbErr(insQual) - ProbErr(delQual)

Parameters:

insQual - PhRED scaled quality/probability of the first event.

delQual - PhRED scaled quality/probability of the second event.

Returns:

a value between 0 and 1.

matchToMatchProbLog10

public static double matchToMatchProbLog10(byte insQual,
                                           byte delQual)

Returns the log10 probability that neither of two events, insertion and deletion, takes place.

We assume that both event never occur together so that the probability of no event is:
1 - ProbErr(insQual) - ProbErr(delQual)

Parameters:

insQual - PhRED scaled quality/probability of an insertion.

delQual - PhRED scaled quality/probability of a deletion.

Returns:

a value between 0 and -Inf.

matchToMatchProb

public static double matchToMatchProb(int insQual,
                                      int delQual)

Returns the probability that neither of two events, insertion and deletion, takes place.

We assume that both event never occur together and that delQual is the conditional probability (qual. encoded) of the second event, given the first event didn't took place. So that the probability of no event is:
1 - ProbErr(insQual) - ProbErr(delQual)

Parameters:

insQual - PhRED scaled quality/probability of an insertion.

delQual - PhRED scaled quality/probability of a deletion.

Returns:

a value between 0 and 1.

matchToMatchProbLog10

public static double matchToMatchProbLog10(int insQual,
                                           int delQual)

Returns the log-probability that neither of two events takes place.

We assume that both events never occur together and that delQual is the conditional probability (qual. encoded) of the second event, given the first event didn't took place. So that the probability of no event is:
1 - ProbErr(insQual) - ProbErr(delQual)

Parameters:

insQual - PhRED scaled quality/probability of an insertion.

delQual - PhRED scaled quality/probability of a deletion.

Returns:

a value between 0 and -Inf.