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