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package bloom;
import java.util.ArrayList;
import java.util.Random;
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 6, 2012
*
*/
public class LargeKmerCount2 {
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=null;
if(fileIO.FileFormat.hasFastaExtension(fname1)){
FastaReadInputStream.MIN_READ_LEN=k;
}
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"+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);
}
long estKmers=load+min(actualCollisions, (long)expectedCollisions);
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("probCollisions:\t \t"+(long)probNewKeyCollisions);
System.out.println("EstimateP: \t \t"+(sum2+(long)probNewKeyCollisions));
System.out.println("expectedColl: \t \t"+(long)expectedCollisions);
System.out.println("actualColl: \t \t"+(long)actualCollisions);
System.out.println("estimateKmers: \t \t"+estKmers);
System.out.println();
System.out.println("Singleton: \t"+Tools.format("%.3f%% ",(100l*x/(double)sum2))+"\t"+x);
x=sum2-x;
System.out.println("Useful: \t"+Tools.format("%.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);
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);
load=0;
probNewKeyCollisions=0;
invCells=1d/cells;
invKmerSpace=Math.pow(0.5, 2*k);
if(cells>=Math.pow(4, k)){invCells=0;}
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);
if(verbose){System.err.println("Started cris");}
cris.start(); //4567
}
boolean paired=cris.paired();
if(verbose){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){
keysCounted++;
if(len>k){kmer=kmer^rotMasks[x2];}
long hashcode=kmer&0x7fffffffffffffffL;
// hashcode=randy.nextLong()&~((-1L)<<(2*k));
long code1=hashcode%(cells-3);
// long code2=((~hashcode)&0x7fffffffffffffffL)%(cells-5);
int value=count.increment2(code1, 1);
double probCollision=load*invCells;
// expectedCollisions+=probCollision;
expectedCollisions+=probCollision*(1-(load+min(expectedCollisions, actualCollisions))*invKmerSpace);
if(value==0){load++;}
else{
actualCollisions++;
double probNewKey=(load*invCells)*expectedCollisions/(min(expectedCollisions, actualCollisions));
double estKeys=load+probNewKeyCollisions;
double probOldKey=estKeys*invKmerSpace;
probNewKeyCollisions+=probNewKey*(1-probOldKey);
// double estKmers=load+min(actualCollisions, expectedCollisions);
// double probOldKmer=estKmers*invKmerSpace;
// probNewKeyCollisions+=(prob*(1-prob2));
}
//// probCollisions+=(load*invCells);
// if(value==0){load++;}
// else{
//// long load2=keysCounted-load;
// double prob=Math.sqrt(load*invCells);
// double estKmers=load+probNewKeyCollisions;
// double prob2=estKmers*invKmerSpace;
//// probCollisions+=(prob*(1-prob2));
//// probCollisions+=Math.sqrt(prob*(1-prob2));
// probNewKeyCollisions+=Math.sqrt(prob*(1-prob2));
//// probCollisions+=min(prob, 1-prob2);
//// probCollisions+=(load*invCells);
// }
}
}
}
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){
keysCounted++;
if(len>k){kmer=kmer^rotMasks[x2];}
long hashcode=kmer&0x7fffffffffffffffL;
// hashcode=randy.nextLong()&~((-1L)<<(2*k));
long code1=hashcode%(cells-3);
// long code2=((~hashcode)&0x7fffffffffffffffL)%(cells-5);
int value=count.increment2(code1, 1);
double probCollision=load*invCells;
// expectedCollisions+=probCollision;
expectedCollisions+=probCollision*(1-(load+min(expectedCollisions, actualCollisions))*invKmerSpace);
if(value==0){load++;}
else{
actualCollisions++;
double probNewKey=(load*invCells)*expectedCollisions/(min(expectedCollisions, actualCollisions));
double estKeys=load+probNewKeyCollisions;
double probOldKey=estKeys*invKmerSpace;
probNewKeyCollisions+=probNewKey*(1-probOldKey);
// double estKmers=load+min(actualCollisions, expectedCollisions);
// double probOldKmer=estKmers*invKmerSpace;
// probNewKeyCollisions+=(prob*(1-prob2));
}
//// probCollisions+=(load*invCells);
// if(value==0){load++;}
// else{
//// long load2=keysCounted-load;
// double prob=Math.sqrt(load*invCells);
// double estKmers=load+probNewKeyCollisions;
// double prob2=estKmers*invKmerSpace;
//// probCollisions+=(prob*(1-prob2));
//// probCollisions+=Math.sqrt(prob*(1-prob2));
// probNewKeyCollisions+=Math.sqrt(prob*(1-prob2));
//// probCollisions+=min(prob, 1-prob2);
//// probCollisions+=(load*invCells);
// }
}
}
}
}
}
//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 final long min(long x, long y){return x<y ? x : y;}
public static final long max(long x, long y){return x>y ? x : y;}
public static final double min(double x, double y){return x<y ? x : y;}
public static final double max(double x, double 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=10000000L;
public static final int ROTATE_DIST=2;
/** Non-empty cells in hash table */
public static long load;
/** Number of expected collisions */
public static double expectedCollisions;
/** Number of actual collisions (possibly by same value) */
public static long actualCollisions;
/** Number of probable collisions caused by new keys */
public static double probNewKeyCollisions;
/** Inverse of hash table size */
public static double invCells;
/** Inverse of number of potential kmers */
public static double invKmerSpace;
/** Inverse of number of potential kmers */
public static long keysCounted;
public static final Random randy=new Random(1);
}
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