jpayne@68: package consensus;
jpayne@68: 
jpayne@68: import structures.ByteBuilder;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Superclass for consensus package classes.
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date September 6, 2019
jpayne@68:  *
jpayne@68:  */
jpayne@68: public abstract class ConsensusObject {
jpayne@68: 
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Methods            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Return the text representation of this object */
jpayne@68: 	public abstract ByteBuilder toText();
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final String toString(){return toText().toString();}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Statics            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	static int minDepth=2;
jpayne@68: 	public static float MAF_sub=0.25f;
jpayne@68: 	public static float MAF_del=0.5f;
jpayne@68: 	public static float MAF_ins=0.5f;
jpayne@68: 	public static float MAF_noref=0.4f;
jpayne@68: 	static boolean onlyConvertNs=false;
jpayne@68: 	static boolean noIndels=false;
jpayne@68: 	public static float trimDepthFraction=0.0f;
jpayne@68: 	public static boolean trimNs=false;
jpayne@68: 	
jpayne@68: 	public static boolean useMapq=false;
jpayne@68: 	public static boolean invertIdentity=false;
jpayne@68: 	public static int identityCeiling=150;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Constants           ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/* Possible types */
jpayne@68: 	/** Match/Sub, neutral-length node or edge to the next REF node */
jpayne@68: 	public static final int REF=2;
jpayne@68: 	/** Insertion node or edge to an insertion node */
jpayne@68: 	public static final int INS=1;
jpayne@68: 	/** Edge to a non-adjacent node */
jpayne@68: 	public static final int DEL=0;
jpayne@68: 	
jpayne@68: 	static final String[] TYPE_NAMES={"DEL", "INS", "REF"};
jpayne@68: 	
jpayne@68: 	public static boolean verbose=false;
jpayne@68: 	
jpayne@68: }