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package cluster;
import java.io.Serializable;
import stream.Read;
/**
* @author Brian Bushnell
* @date Mar 24, 2014
*
*/
class ReadTag implements Serializable{
/**
*
*/
private static final long serialVersionUID = -6186366525723397478L;
public ReadTag(Read r_){
r=r_;
strand=r.strand();
int gcCount_=0;
for(byte b : r.bases){
if(b=='G' || b=='C'){
gcCount_++;
}
}
gcCount=gcCount_;
processHeader(r.id);
}
private void processHeader(String s){
assert(false) : "TODO";
gc=-1;
depth=-1;
cluster0=-1;
}
Read r1(){
return strand==0 ? r : r.mate;
}
Read r2(){
return strand==1 ? r : r.mate;
}
ReadTag tag1(){
return (ReadTag)r1().obj;
}
ReadTag tag2(){
Read r2=r2();
return r2==null ? null : (ReadTag)r2.obj;
}
// private int[] toKmers(final int k){
// return ClusterTools.toKmers(r.bases, null, k);
// }
int[] kmerArray1(int k1){
if(kmerArray1==null){kmerArray1=ClusterTools.toKmers(r.bases, null, k1);}
return kmerArray1;
}
int[] kmerArray2(int k2){
if(kmerArray2==null){kmerArray2=ClusterTools.toKmerCounts(r.bases, null, k2);}
return kmerArray2;
}
float[] kmerFreq2(int k2){
if(kmerFreq2==null){
int[] counts=kmerArray2(k2);
if(counts!=null){
long sum=shared.Vector.sum(counts);
kmerFreq2=new float[counts.length];
float extra=(0.05f/counts.length);
float mult=0.95f/sum;
for(int i=0; i<counts.length; i++){
kmerFreq2[i]=counts[i]*mult+extra;
}
}
}
return kmerFreq2;
}
/** Sorted long kmers */
private int[] kmerArray1;
/** Canonically-ordered short kmer counts */
private int[] kmerArray2;
private float[] kmerFreq2;
final Read r;
final byte strand;
final int gcCount;
int depth;
int cluster0=-1; //initial cluster
int cluster1=-1; //final cluster
float gc;
}
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