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package sort;
import dna.AminoAcid;
import shared.Tools;
import stream.Read;
/**
* @author Brian Bushnell
* @date Oct 27, 2014
*
*/
public class ReadComparatorTopological5Bit extends ReadComparator{
private ReadComparatorTopological5Bit(){}
@Override
public int compare(Read r1, Read r2) {
return ascending*compare(r1, r2, true);
}
public int compare(Read r1, Read r2, boolean compareMates) {
if(r1.numericID!=r2.numericID){return r1.numericID>r2.numericID ? 1 : -1;}
int x=compareVectors(r1.bases, r2.bases, 12);
if(x!=0){return x;}
if(r1.mate!=null && r2.mate!=null){
x=compareVectors(r1.mate.bases, r2.mate.bases, 0);
}
if(x!=0){return x;}
if(r1.bases!=null && r2.bases!=null && r1.length()!=r2.length()){return r1.length()-r2.length();}
if(r1.mate!=null && r2.mate!=null && r1.mate.bases!=null && r2.mate.bases!=null
&& r1.mateLength()!=r2.mateLength()){return r1.mateLength()-r2.mateLength();}
x=compareVectors(r1.quality, r2.quality, 0);
if(x!=0){return 0-x;}
if(r1.mate!=null && r2.mate!=null){
x=compareVectors(r1.mate.quality, r2.mate.quality, 0);
}
if(x!=0){return 0-x;}
return r1.id.compareTo(r2.id);
}
public int compareVectors(final byte[] a, final byte[] b, final int start){
if(a==null || b==null){
if(a==null && b!=null){return 1;}
if(a!=null && b==null){return -1;}
return 0;
}
final int lim=Tools.min(a.length, b.length);
for(int i=start; i<lim; i++){
if(a[i]<b[i]){return -1;}
if(a[i]>b[i]){return 1;}
}
return 0;
}
public int compareVectorsN(final byte[] a, final byte[] b, final int start){
if(a==null || b==null){
if(a==null && b!=null){return 1;}
if(a!=null && b==null){return -1;}
return 0;
}
final int lim=Tools.min(a.length, b.length);
for(int i=start; i<lim; i++){
if(a[i]=='N' && b[i]!='N'){return 1;}
if(a[i]!='N' && b[i]=='N'){return -1;}
if(a[i]<b[i]){return -1;}
if(a[i]>b[i]){return 1;}
}
return 0;
}
public static long genKmer(Read r) {
long kmer=genKmer(r.bases);
r.numericID=kmer;
return kmer;
}
public static long genKmer(byte[] bases){
final byte[] lookup=AminoAcid.symbolTo5Bit;
final int k=12;
final int max=Tools.min(bases.length, 12);
long kmer=0;
for(int i=0; i<max; i++){
byte b=bases[i];
long x=lookup[b];
kmer=((kmer<<5)|x);
}
if(max<k){kmer<<=(5*(k-max));}
assert(kmer>=0);
return kmer;
}
@Override
public void setAscending(boolean asc) {
ascending=(asc ? 1 : -1);
}
public static final ReadComparatorTopological5Bit comparator=new ReadComparatorTopological5Bit();
int ascending=1;
}
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