jpayne@68: package bloom;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.BitSet;
jpayne@68: import java.util.Locale;
jpayne@68: 
jpayne@68: import dna.AminoAcid;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import shared.Timer;
jpayne@68: import stream.ConcurrentReadInputStream;
jpayne@68: import stream.FastaReadInputStream;
jpayne@68: import stream.Read;
jpayne@68: import structures.ListNum;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Jul 5, 2012
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class KmerCount5 extends KmerCountAbstract {
jpayne@68: 	
jpayne@68: 	public static void main(String[] args){
jpayne@68: 
jpayne@68: 		Timer t=new Timer();
jpayne@68: 
jpayne@68: 		String fname1=args[0];
jpayne@68: 		String fname2=(args.length>1 ? args[1] : null);
jpayne@68: 		int k=14;
jpayne@68: 		int cbits=16;
jpayne@68: 		int gap=0;
jpayne@68: 
jpayne@68: 		for(int i=2; i<args.length; i++){
jpayne@68: 			final String arg=args[i];
jpayne@68: 			final String[] split=arg.split("=");
jpayne@68: 			String a=split[0].toLowerCase();
jpayne@68: 			String b=split.length>1 ? split[1] : null;
jpayne@68: 
jpayne@68: 			if(a.equals("k") || a.equals("kmer")){
jpayne@68: 				k=Integer.parseInt(b);
jpayne@68: 			}else if(a.startsWith("cbits") || a.startsWith("cellbits")){
jpayne@68: 				cbits=Integer.parseInt(b);
jpayne@68: 			}else if(a.startsWith("gap")){
jpayne@68: 				gap=Integer.parseInt(b);
jpayne@68: 			}else{
jpayne@68: 				throw new RuntimeException("Unknown parameter "+args[i]);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		KCountArray count=null;
jpayne@68: 		
jpayne@68: 		if(fileIO.FileFormat.hasFastaExtension(fname1)){
jpayne@68: 			assert(!FastaReadInputStream.SPLIT_READS);
jpayne@68: 			FastaReadInputStream.MIN_READ_LEN=k;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		if(gap==0){
jpayne@68: 			count=count(fname1, fname2, k, cbits, true);
jpayne@68: 		}else{
jpayne@68: 			count=countFastqSplit(fname1, fname2, (k+1)/2, k/2, gap, cbits, true, null);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 
jpayne@68: 		t.stop();
jpayne@68: 		System.out.println("Finished counting; time = "+t);
jpayne@68: 
jpayne@68: 		printStatistics(count);
jpayne@68: 
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static void printStatistics(KCountArray count){
jpayne@68: 		long[] freq=count.transformToFrequency();
jpayne@68: 
jpayne@68: 		//		System.out.println(count+"\n");
jpayne@68: 		//		System.out.println(Arrays.toString(freq)+"\n");
jpayne@68: 
jpayne@68: 		long sum=sum(freq);
jpayne@68: 		System.out.println("Kmer fraction:");
jpayne@68: 		int lim1=8, lim2=16;
jpayne@68: 		for(int i=0; i<lim1; i++){
jpayne@68: 			String prefix=i+"";
jpayne@68: 			while(prefix.length()<8){prefix=prefix+" ";}
jpayne@68: 			System.out.println(prefix+"\t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*freq[i]/(double)sum))+"\t"+freq[i]);
jpayne@68: 		}
jpayne@68: 		while(lim1<=freq.length){
jpayne@68: 			int x=0;
jpayne@68: 			for(int i=lim1; i<lim2; i++){
jpayne@68: 				x+=freq[i];
jpayne@68: 			}
jpayne@68: 			String prefix=lim1+"-"+(lim2-1);
jpayne@68: 			if(lim2>=freq.length){prefix=lim1+"+";}
jpayne@68: 			while(prefix.length()<8){prefix=prefix+" ";}
jpayne@68: 			System.out.println(prefix+"\t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*x/(double)sum))+"\t"+x);
jpayne@68: 			lim1*=2;
jpayne@68: 			lim2=min(lim2*2, freq.length);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		long sum2=sum-freq[0];
jpayne@68: 		long x=freq[1];
jpayne@68: 		System.out.println();
jpayne@68: 		System.out.println("Keys Counted:  \t         \t"+keysCounted);
jpayne@68: 		System.out.println("Unique:        \t         \t"+sum2);
jpayne@68: 		System.out.println("Avg Sites/Key: \t         \t"+String.format(Locale.ROOT, "%.3f    ",(keysCounted*1d/sum2)));
jpayne@68: 		System.out.println();
jpayne@68: 		System.out.println("Singleton:     \t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*x/(double)sum2))+"\t"+x);
jpayne@68: 		x=sum2-x;
jpayne@68: 		System.out.println("Useful:        \t"+String.format(Locale.ROOT, "%.3f%%   ",(100l*x/(double)sum2))+"\t"+x);
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static KCountArray count(String reads1, String reads2, int k, int cbits, boolean rcomp){
jpayne@68: 		return count(reads1, reads2, k, cbits, rcomp, null);
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static KCountArray count(String reads1, String reads2, int k, int cbits, boolean rcomp, KCountArray count){
jpayne@68: 		assert(k<32 && k>=1 && (count!=null || k<20));
jpayne@68: 		final int kbits=2*k;
jpayne@68: 		final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
jpayne@68: 
jpayne@68: 		if(count==null){
jpayne@68: 			final long cells=1L<<kbits;
jpayne@68: 			if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
jpayne@68: 			count=KCountArray.makeNew(cells, cbits);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		final ConcurrentReadInputStream cris;
jpayne@68: 		{
jpayne@68: 			FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
jpayne@68: 			FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
jpayne@68: 			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
jpayne@68: 			cris.start(); //4567
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		assert(cris!=null) : reads1;
jpayne@68: 		System.err.println("Started cris");
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		if(verbose){System.err.println("Paired: "+paired);}
jpayne@68: 
jpayne@68: 		ListNum<Read> ln=cris.nextList();
jpayne@68: 		ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68: 
jpayne@68: 		if(reads!=null && !reads.isEmpty()){
jpayne@68: 			Read r=reads.get(0);
jpayne@68: 			assert(paired==(r.mate!=null));
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68: 			//System.err.println("reads.size()="+reads.size());
jpayne@68: 			for(Read r : reads){
jpayne@68: 				readsProcessed++;
jpayne@68: 
jpayne@68: 				addRead(r, count, k, mask, rcomp);
jpayne@68: 				if(r.mate!=null){
jpayne@68: 					addRead(r.mate, count, k, mask, rcomp);
jpayne@68: 				}
jpayne@68: 
jpayne@68: 			}
jpayne@68: 			//System.err.println("returning list");
jpayne@68: 			cris.returnList(ln);
jpayne@68: 			//System.err.println("fetching list");
jpayne@68: 			ln=cris.nextList();
jpayne@68: 			reads=(ln!=null ? ln.list : null);
jpayne@68: 		}
jpayne@68: 		if(verbose){System.err.println("Finished reading");}
jpayne@68: 		cris.returnList(ln);
jpayne@68: 		if(verbose){System.err.println("Returned list");}
jpayne@68: 		cris.close();
jpayne@68: 		if(verbose){System.err.println("Closed stream");}
jpayne@68: 		if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
jpayne@68: 
jpayne@68: 
jpayne@68: 		return count;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 
jpayne@68: 
jpayne@68: 
jpayne@68: 	public static KCountArray count(final String reads1, final String reads2, final int k, final int cbits, final boolean rcomp,
jpayne@68: 			KCountArray counts, final KCountArray trusted, final long maxReads, final int thresh, final int detectStepsize, final boolean conservative){
jpayne@68: 
jpayne@68: 		assert(k<32 && k>=1 && (counts!=null || k<20));
jpayne@68: 		final int kbits=2*k;
jpayne@68: 		final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
jpayne@68: 
jpayne@68: 		//		System.out.println("k="+k+", kbits="+kbits+", mask="+Long.toHexString(mask)+", thresh="+thresh);
jpayne@68: 		//		System.out.println("\ntrusted=\n"+trusted);
jpayne@68: 		//		System.out.println("\ncount=\n"+count);
jpayne@68: 
jpayne@68: 		if(counts==null){
jpayne@68: 			final long cells=1L<<kbits;
jpayne@68: 			if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
jpayne@68: 			counts=KCountArray.makeNew(cells, cbits);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		final ConcurrentReadInputStream cris;
jpayne@68: 		{
jpayne@68: 			FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
jpayne@68: 			FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
jpayne@68: 			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
jpayne@68: 			cris.start(); //4567
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		assert(cris!=null) : reads1;
jpayne@68: 		System.err.println("Started cris");
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		if(verbose){System.err.println("Paired: "+paired);}
jpayne@68: 
jpayne@68: 		ListNum<Read> ln=cris.nextList();
jpayne@68: 		ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68: 
jpayne@68: 		if(reads!=null && !reads.isEmpty()){
jpayne@68: 			Read r=reads.get(0);
jpayne@68: 			assert(paired==(r.mate!=null));
jpayne@68: 		}
jpayne@68: 
jpayne@68: 
jpayne@68: 		while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68: 			//System.err.println("reads.size()="+reads.size());
jpayne@68: 			for(Read r : reads){
jpayne@68: 
jpayne@68: 				Read r2=r.mate;
jpayne@68: 				{
jpayne@68: 					if(trusted!=null){
jpayne@68: 						BitSet bs=(conservative ? ErrorCorrect.detectErrorsBulk(r, trusted, k, thresh, detectStepsize) :
jpayne@68: 							ErrorCorrect.detectTrusted(r, trusted, k, thresh, detectStepsize));
jpayne@68: 						//						System.out.println("\n"+toString(bs, r.length()));
jpayne@68: 						//						System.out.println(new String(r.bases));
jpayne@68: 						for(int i=bs.nextClearBit(0); i<r.length(); i=bs.nextClearBit(i+1)){
jpayne@68: 							r.bases[i]='N';
jpayne@68: 							r.quality[i]=0;
jpayne@68: 						}
jpayne@68: 						//						System.out.println(new String(r.bases));
jpayne@68: 						//						System.out.println("used = "+String.format(Locale.ROOT, "%.3f%%",count.usedFraction()*100));
jpayne@68: 						//						System.out.println("used = "+((KCountArray4)count).cellsUsed());
jpayne@68: 						//						if(bs.length()<r.length()){r=null;}
jpayne@68: 					}
jpayne@68: 					//					if(r!=null){KmerCount5.addRead(r, count, k, mask, rcomp);}
jpayne@68: 					KmerCount5.addRead(r, counts, k, mask, rcomp);
jpayne@68: 				}
jpayne@68: 				if(r2!=null){
jpayne@68: 					if(trusted!=null){
jpayne@68: 						BitSet bs=(conservative ? ErrorCorrect.detectErrorsBulk(r2, trusted, k, thresh, detectStepsize) :
jpayne@68: 							ErrorCorrect.detectTrusted(r2, trusted, k, thresh, detectStepsize));
jpayne@68: 						for(int i=bs.nextClearBit(0); i<r2.length(); i=bs.nextClearBit(i+1)){
jpayne@68: 							r2.bases[i]='N';
jpayne@68: 							r2.quality[i]=0;
jpayne@68: 						}
jpayne@68: 					}
jpayne@68: 					KmerCount5.addRead(r2, counts, k, mask, rcomp);
jpayne@68: 				}
jpayne@68: 
jpayne@68: 			}
jpayne@68: 			//System.err.println("returning list");
jpayne@68: 			cris.returnList(ln);
jpayne@68: 			//System.err.println("fetching list");
jpayne@68: 			ln=cris.nextList();
jpayne@68: 			reads=(ln!=null ? ln.list : null);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		if(verbose){System.err.println("Finished reading");}
jpayne@68: 		cris.returnList(ln);
jpayne@68: 		if(verbose){System.err.println("Returned list");}
jpayne@68: 		cris.close();
jpayne@68: 		if(verbose){System.err.println("Closed stream");}
jpayne@68: 
jpayne@68: 		//		System.out.println("*** after ***");
jpayne@68: 		//		System.out.println("\ntrusted=\n"+trusted);
jpayne@68: 		//		System.out.println("\ncount=\n"+count);
jpayne@68: 
jpayne@68: 		return counts;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 
jpayne@68: 	public static KCountArray countFastqSplit(String reads1, String reads2, int k1, int k2, int gap, int cbits, boolean rcomp, KCountArray counts){
jpayne@68: 		int k=k1+k2;
jpayne@68: 		assert(k<32 && k>=1 && (counts!=null || k<20));
jpayne@68: 		assert(gap>=0);
jpayne@68: 		final int kbits1=2*k1;
jpayne@68: 		final int kbits2=2*k2;
jpayne@68: 		final long mask1=~((-1L)<<(kbits1));
jpayne@68: 		final long mask2=~((-1L)<<(kbits2));
jpayne@68: 
jpayne@68: 		if(counts==null){
jpayne@68: 			final long cells=1L<<(kbits1+kbits2);
jpayne@68: 			if(verbose){System.err.println("k1="+k1+", k2="+k2+", kbits1="+kbits1+", kbits2="+kbits2+", cells="+cells+
jpayne@68: 					", mask1="+Long.toHexString(mask1)+", mask2="+Long.toHexString(mask2));}
jpayne@68: 			counts=KCountArray.makeNew(cells, cbits);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		final ConcurrentReadInputStream cris;
jpayne@68: 		{
jpayne@68: 			FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
jpayne@68: 			FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
jpayne@68: 			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
jpayne@68: 			cris.start(); //4567
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		assert(cris!=null) : reads1;
jpayne@68: 		System.err.println("Started cris");
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		if(verbose){System.err.println("Paired: "+paired);}
jpayne@68: 
jpayne@68: 		ListNum<Read> ln=cris.nextList();
jpayne@68: 		ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68: 
jpayne@68: 		if(reads!=null && !reads.isEmpty()){
jpayne@68: 			Read r=reads.get(0);
jpayne@68: 			assert(paired==(r.mate!=null));
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68: 			//System.err.println("reads.size()="+reads.size());
jpayne@68: 			for(Read r : reads){
jpayne@68: 				readsProcessed++;
jpayne@68: 
jpayne@68: 				addReadSplit(r, counts, k1, k2, mask1, mask2, gap, rcomp);
jpayne@68: 				if(r.mate!=null){
jpayne@68: 					addReadSplit(r.mate, counts, k1, k2, mask1, mask2, gap, rcomp);
jpayne@68: 				}
jpayne@68: 
jpayne@68: 			}
jpayne@68: 			//System.err.println("returning list");
jpayne@68: 			cris.returnList(ln);
jpayne@68: 			//System.err.println("fetching list");
jpayne@68: 			ln=cris.nextList();
jpayne@68: 			reads=(ln!=null ? ln.list : null);
jpayne@68: 		}
jpayne@68: 		if(verbose){System.err.println("Finished reading");}
jpayne@68: 		cris.returnList(ln);
jpayne@68: 		if(verbose){System.err.println("Returned list");}
jpayne@68: 		cris.close();
jpayne@68: 		if(verbose){System.err.println("Closed stream");}
jpayne@68: 		if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
jpayne@68: 
jpayne@68: 
jpayne@68: 		return counts;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static void addRead(final Read r, final KCountArray count, final int k, final long mask, boolean rcomp){
jpayne@68: 		int len=0;
jpayne@68: 		long kmer=0;
jpayne@68: 		byte[] bases=r.bases;
jpayne@68: 		byte[] quals=r.quality;
jpayne@68: 		for(int i=0; i<bases.length; i++){
jpayne@68: 			byte b=bases[i];
jpayne@68: 			int x=AminoAcid.baseToNumber[b];
jpayne@68: 			if(x<0 || (quals!=null && quals[i]<minQuality)){
jpayne@68: 				len=0;
jpayne@68: 				kmer=0;
jpayne@68: 			}else{
jpayne@68: 				kmer=((kmer<<2)|x)&mask;
jpayne@68: 				len++;
jpayne@68: 				if(len>=k){
jpayne@68: 					keysCounted++;
jpayne@68: 					//					System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68: 					count.increment(kmer);
jpayne@68: 					//					System.out.println(" -> "+count.read(kmer));
jpayne@68: 					//					System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
jpayne@68: 					//					array[(int)kmer]++;
jpayne@68: 					//					System.out.println(" -> "+array[(int)kmer]+"\n");
jpayne@68: 					//					assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(rcomp){
jpayne@68: 			r.reverseComplement();
jpayne@68: 			addRead(r, count, k, mask, false);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static void addReadSplit(final Read r, final KCountArray count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
jpayne@68: 		int len=0;
jpayne@68: 		int shift=k2*2;
jpayne@68: 		long kmer1=0;
jpayne@68: 		long kmer2=0;
jpayne@68: 		byte[] bases=r.bases;
jpayne@68: 		byte[] quals=r.quality;
jpayne@68: 
jpayne@68: 		assert(kmer1>=kmer2);
jpayne@68: 
jpayne@68: 		//		assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
jpayne@68: 
jpayne@68: 		for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
jpayne@68: 			int x1=AminoAcid.baseToNumber[bases[i]];
jpayne@68: 			int x2=AminoAcid.baseToNumber[bases[j]];
jpayne@68: 			if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
jpayne@68: 				len=0;
jpayne@68: 				kmer1=0;
jpayne@68: 				kmer2=0;
jpayne@68: 			}else{
jpayne@68: 				kmer1=((kmer1<<2)|x1)&mask1;
jpayne@68: 				kmer2=((kmer2<<2)|x2)&mask2;
jpayne@68: 				len++;
jpayne@68: 				if(len>=k1){
jpayne@68: 					keysCounted++;
jpayne@68: 					//					System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68: 
jpayne@68: 					long key=(kmer1<<shift)|kmer2;
jpayne@68: 					//					System.err.println(Long.toHexString(key));
jpayne@68: 					count.increment(key);
jpayne@68: 					//					System.out.println(" -> "+count.read(kmer));
jpayne@68: 					//					System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
jpayne@68: 					//					array[(int)kmer]++;
jpayne@68: 					//					System.out.println(" -> "+array[(int)kmer]+"\n");
jpayne@68: 					//					assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(rcomp){
jpayne@68: 			r.reverseComplement();
jpayne@68: 			addReadSplit(r, count, k1, k2, mask1, mask2, gap, false);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static void addReadSplit(final byte[] bases, final KCountArray count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
jpayne@68: 		int len=0;
jpayne@68: 		int shift=k2*2;
jpayne@68: 		long kmer1=0;
jpayne@68: 		long kmer2=0;
jpayne@68: 		byte[] quals=null;
jpayne@68: 
jpayne@68: 		assert(kmer1>=kmer2);
jpayne@68: 
jpayne@68: 		//		assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
jpayne@68: 
jpayne@68: 		for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
jpayne@68: 			int x1=AminoAcid.baseToNumber[bases[i]];
jpayne@68: 			int x2=AminoAcid.baseToNumber[bases[j]];
jpayne@68: 			if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
jpayne@68: 				len=0;
jpayne@68: 				kmer1=0;
jpayne@68: 				kmer2=0;
jpayne@68: 			}else{
jpayne@68: 				kmer1=((kmer1<<2)|x1)&mask1;
jpayne@68: 				kmer2=((kmer2<<2)|x2)&mask2;
jpayne@68: 				len++;
jpayne@68: 				if(len>=k1){
jpayne@68: 					keysCounted++;
jpayne@68: 					//					System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68: 
jpayne@68: 					long key=(kmer1<<shift)|kmer2;
jpayne@68: 					System.out.println(Long.toHexString(kmer1));
jpayne@68: 					System.out.println(Long.toHexString(kmer2));
jpayne@68: 					System.out.println(Long.toHexString(key));
jpayne@68: 					count.increment(key);
jpayne@68: 					//					System.out.println(" -> "+count.read(kmer));
jpayne@68: 					//					System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
jpayne@68: 					//					array[(int)kmer]++;
jpayne@68: 					//					System.out.println(" -> "+array[(int)kmer]+"\n");
jpayne@68: 					//					assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(rcomp){
jpayne@68: 			AminoAcid.reverseComplementBasesInPlace(bases);
jpayne@68: 			addReadSplit(bases, count, k1, k2, mask1, mask2, gap, false);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: }