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package sort;
import stream.Read;
import stream.SamLine;
import var2.ScafMap;
/**
* @author Brian Bushnell
* @date November 20, 2016
*
*/
public final class ReadComparatorPosition extends ReadComparator {
private ReadComparatorPosition(){}
@Override
public int compare(Read r1, Read r2) {
int x=compareInner(r1, r2);
return ascending*x;
}
public static int compareInner(Read r1, Read r2) {
int x=compareInner(r1.samline, r2.samline);
if(x!=0){return x;}
if(r1.id==null && r2.id==null){return 0;}
if(r1.id==null){return -1;}
if(r2.id==null){return 1;}
return r1.id.compareTo(r2.id);
}
public static int compareInner(SamLine a, SamLine b) {
if(a.scafnum<0){a.setScafnum(scafMap);}
if(b.scafnum<0){b.setScafnum(scafMap);}
if(a.scafnum!=b.scafnum){return a.scafnum-b.scafnum;}
if(a.pos!=b.pos){return a.pos-b.pos;}
if(a.strand()!=b.strand()){return a.strand()-b.strand();}
if(a.pnext!=b.pnext){return a.pnext-b.pnext;}
if(a.pairnum()!=b.pairnum()){return a.pairnum()-b.pairnum();}
return 0;
}
private int ascending=1;
@Override
public void setAscending(boolean asc){
ascending=(asc ? 1 : -1);
}
public static final ReadComparatorPosition comparator=new ReadComparatorPosition();
public static ScafMap scafMap=null;
}
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