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package sort;
import stream.Read;
/**
* Sorts highest-quality reads first, and longest first on ties.
* @author Brian Bushnell
* @date Nov 9, 2016
*
*/
public final class ReadQualityComparator extends ReadComparator {
private ReadQualityComparator(){}
@Override
public int compare(Read a, Read b) {
int x=compareInner(a, b);
return ascending*x;
}
private static int compareInner(Read a, Read b) {
if(a==b){return 0;}
if(a==null){return 1;}
if(b==null){return -1;}
Read a2=a.mate, b2=b.mate;
int alen=a.length()+a.mateLength();
int blen=b.length()+b.mateLength();
double aerrors=Read.expectedErrors(a.bases, a.quality, true, a.length());
double berrors=Read.expectedErrors(b.bases, b.quality, true, b.length());
if(a2!=null){aerrors+=Read.expectedErrors(a2.bases, a2.quality, true, a2.length());}
if(b2!=null){berrors+=Read.expectedErrors(b2.bases, b2.quality, true, b2.length());}
double arate=aerrors/alen;
double brate=berrors/blen;
if(arate!=brate){return arate>brate ? 1 : -1;}
if(alen!=blen){return blen-alen;}
int x=a.id.compareTo(b.id);
if(x!=0){return x;}
if(a.numericID>b.numericID){return 1;}
if(b.numericID>a.numericID){return -1;}
return 0;
}
public static final ReadQualityComparator comparator=new ReadQualityComparator();
private int ascending=1;
@Override
public void setAscending(boolean asc){
ascending=(asc ? 1 : -1);
}
}
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