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package bloom;
import java.util.ArrayList;
import dna.AminoAcid;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.FastaReadInputStream;
import stream.Read;
import structures.ListNum;
/**
* @author Brian Bushnell
* @date Jul 5, 2012
*
*/
public class KmerCount3 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=Integer.parseInt(args[args.length-2]);
int cbits=Integer.parseInt(args[args.length-1]);
KCountArray2 count=null;
if(fileIO.FileFormat.hasFastaExtension(fname1)){
FastaReadInputStream.MIN_READ_LEN=k;
}
count=countFastq(fname1, fname2, k, cbits);
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"+Tools.format("%.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"+Tools.format("%.3f%% ",(100l*x/(double)sum))+"\t"+x);
lim1*=2;
lim2=min(lim2*2, freq.length);
}
}
public static KCountArray2 countFastq(String reads1, String reads2, int k, int cbits){
assert(k>=1 && k<20);
final int kbits=2*k;
final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
final long cells=mask+1;
if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
final KCountArray2 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();
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];
if(x<0 || quals[i]<minQuality){
len=0;
kmer=0;
}else{
kmer=((kmer<<2)|x)&mask;
len++;
if(len>=k){
// 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(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];
if(x<0 || quals[i]<minQuality){
len=0;
kmer=0;
}else{
kmer=((kmer<<2)|x)&mask;
len++;
if(len>=k){
count.increment(kmer, 1);
}
}
}
}
}
//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;
}
}
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