Package org.snpeff.align
Class VariantRealign
- java.lang.Object
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- org.snpeff.align.VariantRealign
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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
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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
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Constructor Summary
Constructors Constructor Description VariantRealign()
VariantRealign(Variant variant)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getAltRealign()
java.lang.String
getRefRealign()
Variant
getVariantRealigned()
boolean
realign()
Realign variantvoid
realignSeqs()
Realignmentvoid
setAlignLeft()
void
setAlignRight()
void
setDebug(boolean debug)
void
setSequenceAlt(java.lang.String sequenceAlt)
void
setSequenceRef(java.lang.String sequenceRef)
java.lang.String
toString()
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Field Detail
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INITIAL_BASES_MULTIPLIER
public static final int INITIAL_BASES_MULTIPLIER
- See Also:
- Constant Field Values
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INITIAL_BASES_EXTRA
public static final int INITIAL_BASES_EXTRA
- See Also:
- Constant Field Values
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PROGRESSIVE_BASES_MULTIPLIER
public static final int PROGRESSIVE_BASES_MULTIPLIER
- See Also:
- Constant Field Values
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PROGRESSIVE_BASES_EXTRA
public static final int PROGRESSIVE_BASES_EXTRA
- See Also:
- Constant Field Values
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MAX_ITERATIONS
public static final int MAX_ITERATIONS
- See Also:
- Constant Field Values
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Constructor Detail
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VariantRealign
public VariantRealign()
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VariantRealign
public VariantRealign(Variant variant)
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Method Detail
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getAltRealign
public java.lang.String getAltRealign()
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getRefRealign
public java.lang.String getRefRealign()
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getVariantRealigned
public Variant getVariantRealigned()
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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
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realignSeqs
public void realignSeqs()
Realignment
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setAlignLeft
public void setAlignLeft()
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setAlignRight
public void setAlignRight()
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setDebug
public void setDebug(boolean debug)
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setSequenceAlt
public void setSequenceAlt(java.lang.String sequenceAlt)
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setSequenceRef
public void setSequenceRef(java.lang.String sequenceRef)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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