com.milaboratory.core.alignment.kaligner1

Class KMapper

java.lang.Object

com.milaboratory.core.alignment.kaligner1.KMapper

All Implemented Interfaces:

Serializable

public final class KMapper
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(com.milaboratory.core.sequence.NucleotideSequence, int, int) and align(com.milaboratory.core.sequence.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
KMapper(int kValue, int minDistance, int maxDistance, float absoluteMinScore, float relativeMinScore, int minAlignmentLength, float matchScore, float mismatchPenalty, float offsetShiftPenalty, int maxIndels, boolean floatingLeftBound, boolean floatingRightBound) 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.
int	addReference(NucleotideSequence sequence, int offset, int length) Adds new reference sequence to the base of this mapper and returns index assigned to it.
KMappingResult	align(NucleotideSequence sequence) Performs an alignment.
KMappingResult	align(NucleotideSequence sequence, int from, int to) Performs an alignment for a part of the target sequence.
KMappingResult	align(NucleotideSequence sequence, int from, int to, BitArray filter) Performs an alignment for a part of the target sequence.
static KMapper	createFromParameters(KAlignerParameters parameters) Factory method to create KMapper using parametners specified in the KAlignerParameters object.
float	getAbsoluteMinScore() Returns minimal score
int	getKValue() Returns number of nucleotides in kMer (value of k)
int	getMaxDistance() Returns maximal distance between kMer seed positions in target sequence
int	getMaxIndels() Returns maximal number of insertions and deletions
int	getMinDistance() Returns minimal distance between kMer seed positions in target sequence
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
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, 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

KMapper

public KMapper(int kValue,
       int minDistance,
       int maxDistance,
       float absoluteMinScore,
       float relativeMinScore,
       int minAlignmentLength,
       float matchScore,
       float mismatchPenalty,
       float offsetShiftPenalty,
       int maxIndels,
       boolean floatingLeftBound,
       boolean floatingRightBound)

Creates new KMer mapper.

Parameters:

kValue - 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

absoluteMinScore - minimal score

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

minAlignmentLength - minimal alignment length

matchScore - reward for match (must be > 0)

mismatchPenalty - penalty for mismatch (must be < 0)

maxIndels - maximal number of insertions and deletions

floatingLeftBound - true if left bound of alignment could be floating

floatingRightBound - true if right bound of alignment could be floating

Method Detail

createFromParameters

public static KMapper createFromParameters(KAlignerParameters parameters)

Factory method to create KMapper using parametners specified in the KAlignerParameters object.

Parameters:

parameters - parameters instance

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

addReference

public int addReference(NucleotideSequence sequence,
               int offset,
               int length)

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

User can specify a part of a sequence to be indexed (only this part will be identified during the alignment procedure). The offset returned by alignment procedure will be in global sequence coordinates, relative to the beginning of the sequence (not to the specified offset).

Parameters:

sequence - sequence

offset - offset of subsequence to be indexed

length - length of subsequence to be indexed

Returns:

index assigned to the sequence

align

public KMappingResult 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 KMappingResult 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 KMappingResult 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

getKValue

public int getKValue()

Returns number of nucleotides in kMer (value of k)

Returns:

number of nucleotides in kMer (value of k)

getAbsoluteMinScore

public float getAbsoluteMinScore()

Returns minimal score

Returns:

minimal score

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

getMaxIndels

public int getMaxIndels()

Returns maximal number of insertions and deletions

Returns:

maximal number of insertions and deletions

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