jpayne@68: package bloom;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.Locale;
jpayne@68: 
jpayne@68: import dna.AminoAcid;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
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 KmerCount3 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>3 || args[1].contains(".") ? args[1] : null);
jpayne@68: 		int k=Integer.parseInt(args[args.length-2]);
jpayne@68: 		int cbits=Integer.parseInt(args[args.length-1]);
jpayne@68: 		
jpayne@68: 		KCountArray2 count=null;
jpayne@68: 		
jpayne@68: 		if(fileIO.FileFormat.hasFastaExtension(fname1)){
jpayne@68: 			FastaReadInputStream.MIN_READ_LEN=k;
jpayne@68: 		}
jpayne@68: 		count=countFastq(fname1, fname2, k, cbits);
jpayne@68: 		
jpayne@68: 		
jpayne@68: 		t.stop();
jpayne@68: 		System.out.println("Finished counting; time = "+t);
jpayne@68: 		
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: 	
jpayne@68: 	public static KCountArray2 countFastq(String reads1, String reads2, int k, int cbits){
jpayne@68: 		assert(k>=1 && k<20);
jpayne@68: 		final int kbits=2*k;
jpayne@68: 		final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
jpayne@68: 		final long cells=mask+1;
jpayne@68: 		if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
jpayne@68: 		final KCountArray2 count=new KCountArray2(cells, cbits);
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: 		System.err.println("Paired: "+paired);
jpayne@68: 		
jpayne@68: 		long kmer=0; //current kmer
jpayne@68: 		int len=0;  //distance since last contig start or ambiguous base
jpayne@68: 		
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: 					len=0;
jpayne@68: 					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[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: //								System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68: 								count.increment(kmer, 1);
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: 					
jpayne@68: 					if(r.mate!=null){
jpayne@68: 						len=0;
jpayne@68: 						kmer=0;
jpayne@68: 						bases=r.mate.bases;
jpayne@68: 						quals=r.mate.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[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: 									count.increment(kmer, 1);
jpayne@68: 								}
jpayne@68: 							}
jpayne@68: 						}
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: 			System.err.println("Finished reading");
jpayne@68: 			cris.returnList(ln);
jpayne@68: 			System.err.println("Returned list");
jpayne@68: 			ReadWrite.closeStream(cris);
jpayne@68: 			System.err.println("Closed stream");
jpayne@68: 			System.err.println("Processed "+readsProcessed+" reads.");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return count;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: }