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package sort;
import java.util.Comparator;
import stream.Read;
/**
* @author Brian Bushnell
* @date May 30, 2013
*
*/
public final class ReadErrorComparator implements Comparator<Read>{
@Override
public int compare(Read r1, Read r2) {
int a=(r1.errors+(r1.mate==null ? 0 : r1.mate.errors));
int b=(r2.errors+(r2.mate==null ? 0 : r2.mate.errors));
if(a!=b){return a-b;}
a=(r1.length()+(r1.mate==null ? 0 : r1.mateLength()));
b=(r2.length()+(r2.mate==null ? 0 : r2.mateLength()));
if(a!=b){return b-a;}
float a2=(r1.expectedErrors(true, 0)+(r1.mate==null ? 0 : r1.mate.expectedErrors(true, 0)));
float b2=(r2.expectedErrors(true, 0)+(r2.mate==null ? 0 : r2.mate.expectedErrors(true, 0)));
if(a2!=b2){return a2>b2 ? 1 : -1;}
if(r1.numericID<r2.numericID){return -1;}
else if(r1.numericID>r2.numericID){return 1;}
if(!r1.id.equals(r2.id)){return r1.id.compareTo(r2.id);}
return 0;
}
public static final ReadErrorComparator comparator=new ReadErrorComparator();
}
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