1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
|
package sort;
import hiseq.FlowcellCoordinate;
import stream.Read;
/**
* @author Brian Bushnell
* @date Oct 27, 2014
*
*/
public final class ReadComparatorFlowcell extends ReadComparator {
private ReadComparatorFlowcell(){}
@Override
public int compare(Read r1, Read r2) {
int x=compareInner(r1, r2);
return ascending*x;
}
public int compareInner(Read r1, Read r2) {
if(r1.id==null && r2.id==null){return r1.pairnum()-r2.pairnum();}
if(r1.id==null){return -1;}
if(r2.id==null){return 1;}
FlowcellCoordinate fc1=tlc1.get(), fc2=tlc2.get();
if(fc1==null){
fc1=new FlowcellCoordinate();
fc2=new FlowcellCoordinate();
tlc1.set(fc1);
tlc2.set(fc2);
}
fc1.setFrom(r1.id);
fc2.setFrom(r2.id);
int x=fc1.compareTo(fc2);
if(x==0){return r1.pairnum()-r2.pairnum();}
return x;
}
private int ascending=1;
@Override
public void setAscending(boolean asc){
ascending=(asc ? 1 : -1);
}
public ThreadLocal<FlowcellCoordinate> tlc1=new ThreadLocal<FlowcellCoordinate>();
public ThreadLocal<FlowcellCoordinate> tlc2=new ThreadLocal<FlowcellCoordinate>();
public static final ReadComparatorFlowcell comparator=new ReadComparatorFlowcell();
}
|
