public static AlternateCoordinate getMainAlternate ( Variant variant ) { VariantType type ; switch ( variant . getType ( ) ) { case SNP : type = VariantType . SNV ; break ; case MNP : type = VariantType . MNV ; break ; case SV : type = VariantBuilder . inferType ( variant . getReference ( ) , variant . getAlternate ( ) ) ; break ; default : type = variant . getType ( ) ; } return new AlternateCoordinate ( variant . getChromosome ( ) , variant . getStart ( ) , variant . getEnd ( ) , variant . getReference ( ) , variant . getAlternate ( ) , type ) ; }
Get the variant as Alternate Coordinate .