--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/LargeKmerCount.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,242 @@
+package bloom;
+
+import java.util.ArrayList;
+import java.util.Locale;
+
+import dna.AminoAcid;
+import fileIO.ReadWrite;
+import shared.Timer;
+import stream.ConcurrentGenericReadInputStream;
+import stream.FastqReadInputStream;
+import stream.Read;
+import structures.ListNum;
+
+/**
+ * @author Brian Bushnell
+ * @date Jul 6, 2012
+ *
+ */
+public class LargeKmerCount {
+	
+public static void main(String[] args){
+		
+		Timer t=new Timer();
+		
+		String fname1=args[0];
+		String fname2=(args.length>4 || args[1].contains(".") ? args[1] : null);
+		int indexbits=Integer.parseInt(args[args.length-3]);
+		int cbits=Integer.parseInt(args[args.length-2]);
+		int k=Integer.parseInt(args[args.length-1]);
+		
+		KCountArray2 count=countFastq(fname1, fname2, indexbits, cbits, k);
+		t.stop();
+		System.out.println("Finished counting; time = "+t);
+		
+		long[] freq=count.transformToFrequency();
+
+//		System.out.println(count+"\n");
+//		System.out.println(Arrays.toString(freq)+"\n");
+		
+		long sum=sum(freq);
+		System.out.println("Kmer fraction:");
+		int lim1=8, lim2=16;
+		for(int i=0; i<lim1; i++){
+			String prefix=i+"";
+			while(prefix.length()<8){prefix=prefix+" ";}
+			System.out.println(prefix+"\t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*freq[i]/(double)sum))+"\t"+freq[i]);
+		}
+		while(lim1<=freq.length){
+			int x=0;
+			for(int i=lim1; i<lim2; i++){
+				x+=freq[i];
+			}
+			String prefix=lim1+"-"+(lim2-1);
+			if(lim2>=freq.length){prefix=lim1+"+";}
+			while(prefix.length()<8){prefix=prefix+" ";}
+			System.out.println(prefix+"\t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*x/(double)sum))+"\t"+x);
+			lim1*=2;
+			lim2=min(lim2*2, freq.length);
+		}
+		
+		long sum2=sum-freq[0];
+		long x=freq[1];
+		System.out.println();
+		System.out.println("Unique:     \t         \t"+sum2);
+		System.out.println("CollisionsA:\t         \t"+collisionsA);
+		System.out.println("CollisionsB:\t         \t"+collisionsB);
+		
+		double modifier=(collisionsB)/(double)(32*collisionsA+8*collisionsB);
+		
+		System.out.println("Estimate:   \t         \t"+(sum2+collisionsA+collisionsB-(long)(collisionsA*modifier)));
+		System.out.println();
+		System.out.println("Singleton:  \t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*x/(double)sum2))+"\t"+x);
+		x=sum2-x;
+		System.out.println("Useful:     \t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*x/(double)sum2))+"\t"+x);
+		
+	}
+	
+	public static KCountArray2 countFastq(String reads1, String reads2, int indexbits, int cbits, int k){
+		assert(indexbits>=1 && indexbits<40);
+		collisionsA=0;
+		collisionsB=0;
+		final long cells=1L<<indexbits;
+		final int kbits=ROTATE_DIST*k;
+		final int xorShift=kbits%64;
+		final long[] rotMasks=makeRotMasks(xorShift);
+		final int[] buffer=new int[k];
+		if(verbose){System.err.println("k="+k+", kbits="+kbits+", indexbits="+indexbits+", cells="+cells+", cbits="+cbits);}
+		if(verbose){System.err.println("xorShift="+xorShift+", rotMasks[3]="+Long.toHexString(rotMasks[3]));}
+		final KCountArray2 count=new KCountArray2(cells, cbits);
+		
+		FastqReadInputStream fris1=new FastqReadInputStream(reads1, false);
+		FastqReadInputStream fris2=(reads2==null ? null : new FastqReadInputStream(reads2, false));
+		ConcurrentGenericReadInputStream cris=new ConcurrentGenericReadInputStream(fris1, fris2, maxReads);
+		
+		cris.start();
+		System.err.println("Started cris");
+		boolean paired=cris.paired();
+		System.err.println("Paired: "+paired);
+		
+		long kmer=0; //current kmer
+		int len=0;  //distance since last contig start or ambiguous base
+		
+		{
+			ListNum<Read> ln=cris.nextList();
+			ArrayList<Read> reads=(ln!=null ? ln.list : null);
+			
+			if(reads!=null && !reads.isEmpty()){
+				Read r=reads.get(0);
+				assert(paired==(r.mate!=null));
+			}
+			
+			while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
+				//System.err.println("reads.size()="+reads.size());
+				for(Read r : reads){
+					readsProcessed++;
+					
+					len=0;
+					kmer=0;
+					byte[] bases=r.bases;
+					byte[] quals=r.quality;
+					
+					for(int i=0; i<bases.length; i++){
+						byte b=bases[i];
+						int x=AminoAcid.baseToNumber[b];
+						int x2=buffer[len%buffer.length];
+						buffer[len%buffer.length]=x;
+						if(x<0){
+							len=0;
+							kmer=0;
+						}else{
+							kmer=(Long.rotateLeft(kmer,ROTATE_DIST)^x);
+							len++;
+							if(len>=k){
+								if(len>k){kmer=kmer^rotMasks[x2];}
+								long hashcode=kmer&0x7fffffffffffffffL;
+								long code1=hashcode%(cells-3);
+								long code2=((~hashcode)&0x7fffffffffffffffL)%(cells-5);
+								int value=count.increment2(code1, 1);
+								long temp=count.read(code2);
+								if(temp>0){
+									if(value==0){collisionsA++;}
+									else{collisionsB++;}
+								}
+							}
+						}
+					}
+					
+					
+					if(r.mate!=null){
+						len=0;
+						kmer=0;
+						bases=r.mate.bases;
+						quals=r.mate.quality;
+						for(int i=0; i<bases.length; i++){
+							byte b=bases[i];
+							int x=AminoAcid.baseToNumber[b];
+							int x2=buffer[len%buffer.length];
+							buffer[len%buffer.length]=x;
+							if(x<0){
+								len=0;
+								kmer=0;
+							}else{
+								kmer=(Long.rotateLeft(kmer,ROTATE_DIST)^x);
+								len++;
+								if(len>=k){
+									if(len>k){kmer=kmer^rotMasks[x2];}
+									long hashcode=kmer&0x7fffffffffffffffL;
+									long code1=hashcode%(cells-3);
+									long code2=((~hashcode)&0x7fffffffffffffffL)%(cells-5);
+									int value=count.increment2(code1, 1);
+									long temp=count.read(code2);
+									if(temp>0){
+										if(value==0){collisionsA++;}
+										else{collisionsB++;}
+									}
+								}
+							}
+						}
+					}
+					
+				}
+				//System.err.println("returning list");
+				cris.returnList(ln);
+				//System.err.println("fetching list");
+				ln=cris.nextList();
+				reads=(ln!=null ? ln.list : null);
+			}
+			System.err.println("Finished reading");
+			cris.returnList(ln);
+			System.err.println("Returned list");
+			ReadWrite.closeStream(cris);
+			System.err.println("Closed stream");
+			System.err.println("Processed "+readsProcessed+" reads.");
+		}
+		
+		return count;
+	}
+	
+	public static final long[] makeRotMasks(int rotDist){
+		long[] masks=new long[4];
+		for(long i=0; i<4; i++){
+			masks[(int)i]=Long.rotateLeft(i, rotDist);
+		}
+		return masks;
+	}
+	
+	public static long[] transformToFrequency(int[] count){
+		long[] freq=new long[2000];
+		int max=freq.length-1;
+		for(int i=0; i<count.length; i++){
+			int x=count[i];
+			x=min(x, max);
+			freq[x]++;
+		}
+		return freq;
+	}
+	
+	public static long sum(int[] array){
+		long x=0;
+		for(int y : array){x+=y;}
+		return x;
+	}
+	
+	public static long sum(long[] array){
+		long x=0;
+		for(long y : array){x+=y;}
+		return x;
+	}
+	
+	public static final int min(int x, int y){return x<y ? x : y;}
+	public static final int max(int x, int y){return x>y ? x : y;}
+	
+	public static boolean verbose=true;
+	public static byte minQuality=-5;
+	public static long readsProcessed=0;
+	public static long maxReads=1000000L;
+	public static final int ROTATE_DIST=2;
+
+	public static long collisionsA=0;
+	public static long collisionsB=0;
+	
+}