--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/consensus/ConsensusObject.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,58 @@
+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;
+	
+}