Package org.snpeff.align

Class VariantRealign

java.lang.Object

org.snpeff.align.VariantRealign

public class VariantRealign
extends java.lang.Object

Re-align a variant towards the leftmost (rightmost) position Note: We perform a 'progressive' realignment, asking for more reference sequence as we need it

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static int	INITIAL_BASES_EXTRA
static int	INITIAL_BASES_MULTIPLIER
static int	MAX_ITERATIONS
static int	PROGRESSIVE_BASES_EXTRA
static int	PROGRESSIVE_BASES_MULTIPLIER

Constructor Summary

Constructors

Constructor	Description
VariantRealign()
VariantRealign(Variant variant)

Method Summary

Modifier and Type	Method	Description
java.lang.String	getAltRealign()
java.lang.String	getRefRealign()
Variant	getVariantRealigned()
boolean	realign()	Realign variant
void	realignSeqs()	Realignment
void	setAlignLeft()
void	setAlignRight()
void	setDebug(boolean debug)
void	setSequenceAlt(java.lang.String sequenceAlt)
void	setSequenceRef(java.lang.String sequenceRef)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

INITIAL_BASES_MULTIPLIER

public static final int INITIAL_BASES_MULTIPLIER

See Also:

Constant Field Values

INITIAL_BASES_EXTRA

public static final int INITIAL_BASES_EXTRA

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Constant Field Values

PROGRESSIVE_BASES_MULTIPLIER

public static final int PROGRESSIVE_BASES_MULTIPLIER

See Also:

Constant Field Values

PROGRESSIVE_BASES_EXTRA

public static final int PROGRESSIVE_BASES_EXTRA

See Also:

Constant Field Values

MAX_ITERATIONS

public static final int MAX_ITERATIONS

See Also:

Constant Field Values

Constructor Detail

VariantRealign

public VariantRealign()

VariantRealign

public VariantRealign(Variant variant)

Method Detail

getAltRealign

public java.lang.String getAltRealign()

getRefRealign

public java.lang.String getRefRealign()

getVariantRealigned

public Variant getVariantRealigned()

realign

public boolean realign()

Realign variant

Returns:

true if variant was realigned and a new variant (different than the original one) was created. false if it wasn't realigned or there was an error

realignSeqs

public void realignSeqs()

Realignment

setAlignLeft

public void setAlignLeft()

setAlignRight

public void setAlignRight()

setDebug

public void setDebug(boolean debug)

setSequenceAlt

public void setSequenceAlt(java.lang.String sequenceAlt)

setSequenceRef

public void setSequenceRef(java.lang.String sequenceRef)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object