Package org.snpeff.interval.codonChange
Class CodonChangeMixed
java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeMnp
org.snpeff.interval.codonChange.CodonChangeMixed
Calculate codon changes produced by a 'mixed' variant
Essentially every 'mixed' variant can be represented as a concatenation of a SNP/MNP + an INS/DEL
- Author:
- pcingola
-
Field Summary
FieldsFields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
-
Constructor Summary
ConstructorsConstructorDescriptionCodonChangeMixed
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Method Summary
Methods inherited from class org.snpeff.interval.codonChange.CodonChangeMnp
codonOldNew, codonsAlt, codonsRef, netCdsChange
Methods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonChange, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, toString
-
Field Details
-
debug
public static boolean debug
-
-
Constructor Details
-
CodonChangeMixed
-
-
Method Details
-
codonChange
public void codonChange()Description copied from class:CodonChangeMnp
Calculate a list of codon changes- Overrides:
codonChange
in classCodonChangeMnp
-