--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KmerCount4.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,358 @@
+package bloom;
+
+import java.util.ArrayList;
+import java.util.Locale;
+
+import dna.AminoAcid;
+import fileIO.FileFormat;
+import shared.Timer;
+import stream.ConcurrentReadInputStream;
+import stream.FastaReadInputStream;
+import stream.Read;
+import structures.ListNum;
+
+/**
+ * @author Brian Bushnell
+ * @date Jul 5, 2012
+ *
+ */
+public class KmerCount4 extends KmerCountAbstract {
+	
+	public static void main(String[] args){
+		
+		Timer t=new Timer();
+		
+		String fname1=args[0];
+		String fname2=(args.length>3 || args[1].contains(".") ? args[1] : null);
+		int k=14;
+		int cbits=16;
+		int gap=0;
+		
+		for(int i=(fname2==null ? 1 : 2); i<args.length; i++){
+			final String arg=args[i];
+			final String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+
+			if(a.equals("k") || a.equals("kmer")){
+				k=Integer.parseInt(b);
+			}else if(a.startsWith("cbits") || a.startsWith("cellbits")){
+				cbits=Integer.parseInt(b);
+			}else if(a.startsWith("gap")){
+				gap=Integer.parseInt(b);
+			}else{
+				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		
+		KCountArray2 count=null;
+		
+		if(fileIO.FileFormat.hasFastaExtension(fname1)){
+			assert(!FastaReadInputStream.SPLIT_READS);
+			FastaReadInputStream.MIN_READ_LEN=k;
+		}
+		
+		if(gap==0){
+			count=count(fname1, fname2, k, cbits, true);
+		}else{
+			count=countFastqSplit(fname1, fname2, (k+1)/2, k/2, gap, cbits, true, null);
+		}
+		
+		
+		t.stop();
+		System.out.println("Finished counting; time = "+t);
+		
+		printStatistics(count);
+		
+	}
+
+	public static void printStatistics(KCountArray2 count){
+		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("Keys Counted:  \t         \t"+keysCounted);
+		System.out.println("Unique:        \t         \t"+sum2);
+		System.out.println("Avg Sites/Key: \t         \t"+String.format(Locale.ROOT, "%.3f    ",(keysCounted*1d/sum2)));
+		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 count(String reads1, String reads2, int k, int cbits, boolean rcomp){
+		return count(reads1, reads2, k, cbits, rcomp, null);
+	}
+	
+	public static KCountArray2 count(String reads1, String reads2, int k, int cbits, boolean rcomp, KCountArray2 count){
+		assert(k>=1 && k<20);
+		final int kbits=2*k;
+		final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
+		
+		if(count==null){
+			final long cells=1L<<kbits;
+			if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
+			count=new KCountArray2(cells, cbits);
+		}
+		
+		final ConcurrentReadInputStream cris;
+		{
+			FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
+			FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
+			cris.start(); //4567
+		}
+		
+		assert(cris!=null) : reads1;
+		System.err.println("Started cris");
+		boolean paired=cris.paired();
+		if(verbose){System.err.println("Paired: "+paired);}
+		
+		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++;
+
+				addRead(r, count, k, mask, rcomp);
+				if(r.mate!=null){
+					addRead(r.mate, count, k, mask, rcomp);
+				}
+
+			}
+			//System.err.println("returning list");
+			cris.returnList(ln);
+			//System.err.println("fetching list");
+			ln=cris.nextList();
+			reads=(ln!=null ? ln.list : null);
+		}
+		if(verbose){System.err.println("Finished reading");}
+		cris.returnList(ln);
+		if(verbose){System.err.println("Returned list");}
+		cris.close();
+		if(verbose){System.err.println("Closed stream");}
+		if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
+
+		
+		return count;
+	}
+	
+	public static KCountArray2 countFastqSplit(String reads1, String reads2, int k1, int k2, int gap, int cbits, boolean rcomp, KCountArray2 count){
+		assert(k1+k2>=1 && k1+k2<20);
+		assert(gap>=0);
+		final int kbits1=2*k1;
+		final int kbits2=2*k2;
+		final long mask1=~((-1L)<<(kbits1));
+		final long mask2=~((-1L)<<(kbits2));
+		
+		if(count==null){
+			final long cells=1L<<(kbits1+kbits2);
+			if(verbose){System.err.println("k1="+k1+", k2="+k2+", kbits1="+kbits1+", kbits2="+kbits2+", cells="+cells+
+					", mask1="+Long.toHexString(mask1)+", mask2="+Long.toHexString(mask2));}
+			count=new KCountArray2(cells, cbits, gap);
+		}
+		assert(count.gap==gap);
+		
+		final ConcurrentReadInputStream cris;
+		{
+			FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
+			FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
+			cris.start(); //4567
+		}
+		
+		assert(cris!=null) : reads1;
+		System.err.println("Started cris");
+		boolean paired=cris.paired();
+		if(verbose){System.err.println("Paired: "+paired);}
+		
+		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++;
+
+				addReadSplit(r, count, k1, k2, mask1, mask2, gap, rcomp);
+				if(r.mate!=null){
+					addReadSplit(r.mate, count, k1, k2, mask1, mask2, gap, rcomp);
+				}
+
+			}
+			//System.err.println("returning list");
+			cris.returnList(ln);
+			//System.err.println("fetching list");
+			ln=cris.nextList();
+			reads=(ln!=null ? ln.list : null);
+		}
+		if(verbose){System.err.println("Finished reading");}
+		cris.returnList(ln);
+		if(verbose){System.err.println("Returned list");}
+		cris.close();
+		if(verbose){System.err.println("Closed stream");}
+		if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
+
+		
+		return count;
+	}
+	
+	public static void addRead(final Read r, final KCountArray2 count, final int k, final long mask, boolean rcomp){
+		int len=0;
+		long 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];
+			if(x<0 || (quals!=null && quals[i]<minQuality)){
+				len=0;
+				kmer=0;
+			}else{
+				kmer=((kmer<<2)|x)&mask;
+				len++;
+				if(len>=k){
+					keysCounted++;
+//					System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
+					count.increment(kmer, 1);
+//					System.out.println(" -> "+count.read(kmer));
+//					System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
+//					array[(int)kmer]++;
+//					System.out.println(" -> "+array[(int)kmer]+"\n");
+//					assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
+				}
+			}
+		}
+		if(rcomp){
+			r.reverseComplement();
+			addRead(r, count, k, mask, false);
+		}
+	}
+	
+	public static void addReadSplit(final Read r, final KCountArray2 count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
+		int len=0;
+		int shift=k2*2;
+		long kmer1=0;
+		long kmer2=0;
+		byte[] bases=r.bases;
+		byte[] quals=r.quality;
+		
+		assert(kmer1>=kmer2);
+		
+//		assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
+		
+		for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
+			int x1=AminoAcid.baseToNumber[bases[i]];
+			int x2=AminoAcid.baseToNumber[bases[j]];
+			if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
+				len=0;
+				kmer1=0;
+				kmer2=0;
+			}else{
+				kmer1=((kmer1<<2)|x1)&mask1;
+				kmer2=((kmer2<<2)|x2)&mask2;
+				len++;
+				if(len>=k1){
+					keysCounted++;
+//					System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
+					
+					long key=(kmer1<<shift)|kmer2;
+//					System.err.println(Long.toHexString(key));
+					count.increment(key, 1);
+//					System.out.println(" -> "+count.read(kmer));
+//					System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
+//					array[(int)kmer]++;
+//					System.out.println(" -> "+array[(int)kmer]+"\n");
+//					assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
+				}
+			}
+		}
+		if(rcomp){
+			r.reverseComplement();
+			addReadSplit(r, count, k1, k2, mask1, mask2, gap, false);
+		}
+	}
+	
+	public static void addReadSplit(final byte[] bases, final KCountArray2 count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
+		int len=0;
+		int shift=k2*2;
+		long kmer1=0;
+		long kmer2=0;
+		byte[] quals=null;
+		
+		assert(kmer1>=kmer2);
+		
+//		assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
+		
+		for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
+			int x1=AminoAcid.baseToNumber[bases[i]];
+			int x2=AminoAcid.baseToNumber[bases[j]];
+			if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
+				len=0;
+				kmer1=0;
+				kmer2=0;
+			}else{
+				kmer1=((kmer1<<2)|x1)&mask1;
+				kmer2=((kmer2<<2)|x2)&mask2;
+				len++;
+				if(len>=k1){
+					keysCounted++;
+//					System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
+					
+					long key=(kmer1<<shift)|kmer2;
+					System.out.println(Long.toHexString(kmer1));
+					System.out.println(Long.toHexString(kmer2));
+					System.out.println(Long.toHexString(key));
+					count.increment(key, 1);
+//					System.out.println(" -> "+count.read(kmer));
+//					System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
+//					array[(int)kmer]++;
+//					System.out.println(" -> "+array[(int)kmer]+"\n");
+//					assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
+				}
+			}
+		}
+		if(rcomp){
+			AminoAcid.reverseComplementBasesInPlace(bases);
+			addReadSplit(bases, count, k1, k2, mask1, mask2, gap, false);
+		}
+	}
+	
+}