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package bloom;
import java.util.ArrayList;
import java.util.Arrays;
import dna.AminoAcid;
import fileIO.ReadWrite;
import shared.Timer;
import stream.ConcurrentGenericReadInputStream;
import stream.FastqReadInputStream;
import stream.Read;
import structures.ListNum;
/**
* @author Brian Bushnell
* @date Jul 5, 2012
*
*/
public class TestLargeKmer {
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 k=Integer.parseInt(args[args.length-3]);
int cbits=Integer.parseInt(args[args.length-2]);
int k2=Integer.parseInt(args[args.length-1]);
KCountArray2 counts=KmerCount3.countFastq(fname1, fname2, k, cbits);
long[] counts2=countK2(fname1, fname2, k, counts, k2);
t.stop();
System.out.println("Finished counting; time = "+t+"\n");
for(int i=0; i<counts2.length; i++){
System.out.println(i+":\t"+counts2[i]);
}
}
public static long[] countK2(String fname1, String fname2, int k, int cbits, int k2){
KCountArray2 counts=KmerCount3.countFastq(fname1, fname2, k, cbits);
return countK2(fname1, fname2, k, counts, k2);
}
public static long[] countK2(String fname1, String fname2, int k, KCountArray2 counts1, int k2){
assert(k>=1 && k<20);
final int kbits=2*k;
final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
FastqReadInputStream fris1=new FastqReadInputStream(fname1, false);
FastqReadInputStream fris2=(fname2==null ? null : new FastqReadInputStream(fname2, false));
ConcurrentGenericReadInputStream cris=new ConcurrentGenericReadInputStream(fris1, fris2, KmerCount3.maxReads);
cris.start();
System.err.println("Started cris");
boolean paired=cris.paired();
long kmer=0; //current kmer
int len=0; //distance since last contig start or ambiguous base
final long[] upperBound=new long[BOUND_LEN]; //Lowest upper bound provable of kmer count
final int[] ring=new int[k2-k+1];
final int[] subcount=new int[BOUND_LEN];
final int maxValue=subcount.length-1;
{
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){
len=0;
kmer=0;
Arrays.fill(subcount, 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 ringpos=i%ring.length;
int old=ring[ringpos];
int value=0;
if(x<0 || quals[i]<KmerCount3.minQuality){
len=0;
kmer=0;
}else{
kmer=((kmer<<2)|x)&mask;
len++;
if(len>=k){
value=counts1.read(kmer);
}
}
value=min(value, maxValue);
ring[ringpos]=value;
subcount[value]++;
if(i>=ring.length){
subcount[old]--;
}
if(len>=k2){
int sub=0;
while(sub<subcount.length && subcount[sub]==0){sub++;}
assert(sub<subcount.length);
upperBound[sub]++;
}
}
if(r.mate!=null){
bases=r.mate.bases;
quals=r.mate.quality;
len=0;
kmer=0;
Arrays.fill(subcount, 0);
for(int i=0; i<bases.length; i++){
byte b=bases[i];
int x=AminoAcid.baseToNumber[b];
int ringpos=i%ring.length;
int old=ring[ringpos];
int value=0;
if(x<0 || quals[i]<KmerCount3.minQuality){
len=0;
kmer=0;
}else{
kmer=((kmer<<2)|x)&mask;
len++;
if(len>=k){
value=counts1.read(kmer);
}
}
value=min(value, maxValue);
ring[ringpos]=value;
subcount[value]++;
if(i>=ring.length){
subcount[old]--;
}
if(len>=k2){
int sub=0;
while(sub<subcount.length && subcount[sub]==0){sub++;}
assert(sub<subcount.length);
upperBound[sub]++;
}
}
}
}
//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.closeStreams(cris);
System.err.println("Closed stream");
}
return upperBound;
}
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 int BOUND_LEN=256;
}
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