1 package consensus; 2 3 import structures.ByteBuilder; 4 5 /** 6 * Superclass for consensus package classes. 7 * 8 * @author Brian Bushnell 9 * @date September 6, 2019 10 * 11 */ 12 public abstract class ConsensusObject { 13 14 /*--------------------------------------------------------------*/ 15 /*---------------- Methods ----------------*/ 16 /*--------------------------------------------------------------*/ 17 18 /** Return the text representation of this object */ toText()19 public abstract ByteBuilder toText(); 20 21 @Override toString()22 public final String toString(){return toText().toString();} 23 24 /*--------------------------------------------------------------*/ 25 /*---------------- Statics ----------------*/ 26 /*--------------------------------------------------------------*/ 27 28 static int minDepth=2; 29 public static float MAF_sub=0.25f; 30 public static float MAF_del=0.5f; 31 public static float MAF_ins=0.5f; 32 public static float MAF_noref=0.4f; 33 static boolean onlyConvertNs=false; 34 static boolean noIndels=false; 35 public static float trimDepthFraction=0.0f; 36 public static boolean trimNs=false; 37 38 public static boolean useMapq=false; 39 public static boolean invertIdentity=false; 40 public static int identityCeiling=150; 41 42 /*--------------------------------------------------------------*/ 43 /*---------------- Constants ----------------*/ 44 /*--------------------------------------------------------------*/ 45 46 /* Possible types */ 47 /** Match/Sub, neutral-length node or edge to the next REF node */ 48 public static final int REF=2; 49 /** Insertion node or edge to an insertion node */ 50 public static final int INS=1; 51 /** Edge to a non-adjacent node */ 52 public static final int DEL=0; 53 54 static final String[] TYPE_NAMES={"DEL", "INS", "REF"}; 55 56 public static boolean verbose=false; 57 58 } 59