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