com.milaboratory.core.alignment.kaligner2

Class KMapper2

java.lang.Object

com.milaboratory.core.alignment.kaligner2.KMapper2

All Implemented Interfaces:

Serializable

public final class KMapper2
extends Object
implements Serializable

KMapper - class to perform fast alignment based only on matches between kMers of target and one of reference sequences. Alignment performed using seed-and-vote procedure.

align(NucleotideSequence, int, int) and align(NucleotideSequence) methods of this object are thread-safe and can be concurrently used by several threads if no new sequences added after its first invocation.

Algorithm inspired by: Liao Y et al. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013 May 1;41(10):e108. doi: 10.1093/nar/gkt214. Epub 2013 Apr 4.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	SEED_NOT_FOUND_OFFSET

Constructor Summary

Constructors

Constructor and Description
KMapper2(int nValue, int kValue, int minDistance, int maxDistance, int absoluteMinClusterScore, int extraClusterScore, int absoluteMinScore, float relativeMinScore, int matchScore, int mismatchScore, int offsetShiftScore, int slotCount, int maxClusters, int maxClusterIndels, int kMersPerPosition, boolean floatingLeftBound, boolean floatingRightBound) Creates new KMer mapper.
KMapper2(int nValue, int kValue, int minDistance, int maxDistance, int absoluteMinClusterScore, int extraClusterScore, int absoluteMinScore, float relativeMinScore, int matchScore, int mismatchScore, int offsetShiftScore, int slotCount, int maxClusters, int maxClusterIndels, int kMersPerPosition, boolean floatingLeftBound, boolean floatingRightBound, KAligner2Statistics stat) Creates new KMer mapper.

Method Summary

Methods

Modifier and Type	Method and Description
int	addReference(NucleotideSequence sequence) Adds new reference sequence to the base of this mapper and returns index assigned to it.
KMappingResult2	align(NucleotideSequence sequence) Performs an alignment.
KMappingResult2	align(NucleotideSequence sequence, int from, int to) Performs an alignment for a part of the target sequence.
KMappingResult2	align(NucleotideSequence sequence, int from, int to, BitArray filter) Performs an alignment for a part of the target sequence.
KMappingHit2	calculateHit(int id, IntArrayList data, IntArrayList seedPositions) Array list wrapper for calculateHit(int, int[], int, int, IntArrayList).
static KMapper2	createFromParameters(KAlignerParameters2 parameters) Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.
static KMapper2	createFromParameters(KAlignerParameters2 parameters, KAligner2Statistics stat) Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.
protected void	finalize()
int	getAbsoluteMinClusterScore() Returns minimal score for the cluster
int	getExtraClusterScore()
int	getKValue()
int	getMaxDistance() Returns maximal distance between kMer seed positions in target sequence
int	getMinDistance() Returns minimal distance between kMer seed positions in target sequence
int	getNValue() Returns number of nucleotides in kMer (value of k)
org.apache.commons.math3.stat.descriptive.SummaryStatistics	getRecordSizeSummaryStatistics() Method used internally.
float	getRelativeMinScore() Returns maximal ratio between best hit score and other hits scores in returned result
static int	positionInTarget(IntArrayList seedPositions, int record)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

SEED_NOT_FOUND_OFFSET

public static final int SEED_NOT_FOUND_OFFSET

See Also:

Constant Field Values

Constructor Detail

KMapper2

public KMapper2(int nValue,
        int kValue,
        int minDistance,
        int maxDistance,
        int absoluteMinClusterScore,
        int extraClusterScore,
        int absoluteMinScore,
        float relativeMinScore,
        int matchScore,
        int mismatchScore,
        int offsetShiftScore,
        int slotCount,
        int maxClusters,
        int maxClusterIndels,
        int kMersPerPosition,
        boolean floatingLeftBound,
        boolean floatingRightBound)

Creates new KMer mapper.

Parameters:

nValue - nucleotides in kMer (value of k)

minDistance - minimal distance between kMer seed positions in target sequence

maxDistance - maximal distance between kMer seed positions in target sequence

absoluteMinClusterScore - minimal score

relativeMinScore - maximal ratio between best hit score and other hits scores in returned result

matchScore - reward for match (must be > 0)

mismatchScore - penalty for mismatch (must be < 0)

floatingLeftBound - true if left bound of alignment could be floating

floatingRightBound - true if right bound of alignment could be floating

KMapper2

public KMapper2(int nValue,
        int kValue,
        int minDistance,
        int maxDistance,
        int absoluteMinClusterScore,
        int extraClusterScore,
        int absoluteMinScore,
        float relativeMinScore,
        int matchScore,
        int mismatchScore,
        int offsetShiftScore,
        int slotCount,
        int maxClusters,
        int maxClusterIndels,
        int kMersPerPosition,
        boolean floatingLeftBound,
        boolean floatingRightBound,
        KAligner2Statistics stat)

Creates new KMer mapper.

Parameters:

nValue - nucleotides in kMer (value of k)

minDistance - minimal distance between kMer seed positions in target sequence

maxDistance - maximal distance between kMer seed positions in target sequence

absoluteMinClusterScore - minimal score

relativeMinScore - maximal ratio between best hit score and other hits scores in returned result

matchScore - reward for match (must be > 0)

mismatchScore - penalty for mismatch (must be < 0)

floatingLeftBound - true if left bound of alignment could be floating

floatingRightBound - true if right bound of alignment could be floating

stat - stat

Method Detail

createFromParameters

public static KMapper2 createFromParameters(KAlignerParameters2 parameters)

Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.

Parameters:

parameters - parameters instance

Returns:

new KMapper

createFromParameters

public static KMapper2 createFromParameters(KAlignerParameters2 parameters,
                            KAligner2Statistics stat)

Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.

Parameters:

parameters - parameters instance

stat - stat

Returns:

new KMapper

addReference

public int addReference(NucleotideSequence sequence)

Adds new reference sequence to the base of this mapper and returns index assigned to it.

Parameters:

sequence - sequence

Returns:

index assigned to the sequence

align

public KMappingResult2 align(NucleotideSequence sequence)

Performs an alignment.

This methods is thread-safe and can be concurrently used by several threads if no new sequences added after its first invocation.

Parameters:

sequence - target sequence

Returns:

a list of hits found in the target sequence

align

public KMappingResult2 align(NucleotideSequence sequence,
                    int from,
                    int to)

Performs an alignment for a part of the target sequence.

This methods is thread-safe and can be concurrently used by several threads if no new sequences added after its first invocation.

Parameters:

sequence - target sequence

from - first nucleotide to align (inclusive)

to - last nucleotide to align (exclusive)

Returns:

a list of hits found in the target sequence

align

public KMappingResult2 align(NucleotideSequence sequence,
                    int from,
                    int to,
                    BitArray filter)

Performs an alignment for a part of the target sequence.

This methods is thread-safe and can be concurrently used by several threads if no new sequences added after its first invocation.

Parameters:

sequence - target sequence

from - first nucleotide to align (inclusive)

to - last nucleotide to align (exclusive)

filter - record filter (align only records with filter[id] == true)

Returns:

a list of hits found in the target sequence

calculateHit

public KMappingHit2 calculateHit(int id,
                        IntArrayList data,
                        IntArrayList seedPositions)

Array list wrapper for calculateHit(int, int[], int, int, IntArrayList).

positionInTarget

public static int positionInTarget(IntArrayList seedPositions,
                   int record)

getNValue

public int getNValue()

Returns number of nucleotides in kMer (value of k)

Returns:

number of nucleotides in kMer (value of k)

getKValue

public int getKValue()

getAbsoluteMinClusterScore

public int getAbsoluteMinClusterScore()

Returns minimal score for the cluster

Returns:

minimal score for the cluster

getExtraClusterScore

public int getExtraClusterScore()

getMaxDistance

public int getMaxDistance()

Returns maximal distance between kMer seed positions in target sequence

Returns:

maximal distance between kMer seed positions in target sequence

getMinDistance

public int getMinDistance()

Returns minimal distance between kMer seed positions in target sequence

Returns:

minimal distance between kMer seed positions in target sequence

getRelativeMinScore

public float getRelativeMinScore()

Returns maximal ratio between best hit score and other hits scores in returned result

Returns:

maximal ratio between best hit score and other hits scores in returned result

getRecordSizeSummaryStatistics

public org.apache.commons.math3.stat.descriptive.SummaryStatistics getRecordSizeSummaryStatistics()

Method used internally.

toString

public String toString()

Overrides:

toString in class Object

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable