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
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
package sort;
import shared.Tools;
import stream.Read;
/**
* @author Brian Bushnell
* @date Oct 27, 2014
*
*/
public class ReadComparatorTopological extends ReadComparator{
private ReadComparatorTopological(){}
@Override
public int compare(Read r1, Read r2) {
return ascending*compare(r1, r2, true);
}
public int compare(Read r1, Read r2, boolean compareMates) {
int x=compareVectors(r1.bases, r2.bases);
if(x!=0){return x;}
if(r1.mate!=null && r2.mate!=null){
x=compareVectors(r1.mate.bases, r2.mate.bases);
}
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);
if(x!=0){return 0-x;}
if(r1.mate!=null && r2.mate!=null){
x=compareVectors(r1.mate.quality, r2.mate.quality);
}
if(x!=0){return 0-x;}
if(r1.numericID!=r2.numericID){return r1.numericID>r2.numericID ? 1 : -1;}
return r1.id.compareTo(r2.id);
}
public int compareVectors(final byte[] a, final byte[] b){
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=0; 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){
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=0; 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;
}
@Override
public void setAscending(boolean asc) {
ascending=(asc ? 1 : -1);
}
public static final ReadComparatorTopological comparator=new ReadComparatorTopological();
int ascending=1;
}
|
