Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/consensus/ConsensusObject.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
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 */
19 public abstract ByteBuilder toText();
20
21 @Override
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 }