--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/Hasher.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,75 @@
+package clump;
+
+import java.util.Random;
+
+import shared.Tools;
+import stream.Read;
+
+public class Hasher {
+
+	private static synchronized long[][] makeCodes2(int modes){
+		long[][] r=makeCodes(128, modes);
+		
+		for(int i=0; i<26; i++){
+			char c=(char)('A'+i);
+			r[Tools.toLowerCase(c)]=r[c];
+		}
+		return r;
+	}
+	
+	private static synchronized long[][] makeCodes(int symbols, int modes){
+		Random randy=new Random(1);
+		long[][] r=new long[symbols][modes];
+		for(int i=0; i<symbols; i++){
+			for(int j=0; j<modes; j++){
+				r[i][j]=randy.nextLong();
+			}
+		}
+		return r;
+	}
+	
+	public static long hash(byte[] bases){
+		long code=bases.length;
+		for(int i=0; i<bases.length; i++){
+			byte b=bases[i];
+			int mode=(int)(code&31);
+			assert(hashcodes[b]!=null) : "Invalid sequence character: '"+(char)b+"'";
+			code=code^hashcodes[b][mode];
+			code=Long.rotateLeft(code, 1);
+		}
+		return code;
+	}
+	
+	public static final long hash(Read r){
+		return hash(r.bases);
+	}
+	
+	public static final long hashPair(Read r){
+		long a=hash(r);
+		if(r.mate==null){return a;}
+		long b=hash(r.mate);
+		return a^Long.rotateLeft(b, 1);
+	}
+	
+	public static final boolean equalsPaired(Read a, Read b){
+		return equals(a, b) && equals(a.mate, b.mate);
+	}
+	
+	public static final boolean equals(Read a, Read b){
+		if(a==b){return true;}
+		if(a==null || b==null){
+			assert(a!=null || b!=null);
+			return false;
+		}
+		if(a.length()!=b.length()){return false;}
+		if(a.length()==0){return true;}
+		byte[] ab=a.bases, bb=b.bases;
+		for(int i=0; i<ab.length; i++){
+			if(ab[i]!=bb[i]){return false;}
+		}
+		return true;
+	}
+	
+	private static final long[][] hashcodes=makeCodes2(32);
+	
+}