Package org.snpeff.align
Class VariantRealign
java.lang.Object
org.snpeff.align.VariantRealign
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
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
realign()
Realign variantvoid
Realignmentvoid
void
void
setDebug
(boolean debug) void
setSequenceAlt
(String sequenceAlt) void
setSequenceRef
(String sequenceRef) toString()
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Field Details
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INITIAL_BASES_MULTIPLIER
public static final int INITIAL_BASES_MULTIPLIER- See Also:
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INITIAL_BASES_EXTRA
public static final int INITIAL_BASES_EXTRA- See Also:
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PROGRESSIVE_BASES_MULTIPLIER
public static final int PROGRESSIVE_BASES_MULTIPLIER- See Also:
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PROGRESSIVE_BASES_EXTRA
public static final int PROGRESSIVE_BASES_EXTRA- See Also:
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MAX_ITERATIONS
public static final int MAX_ITERATIONS- See Also:
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Constructor Details
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VariantRealign
public VariantRealign() -
VariantRealign
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Method Details
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getAltRealign
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getRefRealign
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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 -
setAlignLeft
public void setAlignLeft() -
setAlignRight
public void setAlignRight() -
setDebug
public void setDebug(boolean debug) -
setSequenceAlt
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setSequenceRef
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toString
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