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
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
|
package sort;
import java.util.Comparator;
import shared.Shared;
import shared.Tools;
import stream.Read;
/**
* @author Brian Bushnell
* @date Oct 27, 2014
*
*/
public class ReadComparatorMapping implements Comparator<Read> {
@Override
public int compare(Read a, Read b) {
if(a.mate==null){
int x=compare2(a, b);
if(x!=0){return x;}
return compare3(a, b);
}else{
if(a.mapped() && b.mapped()){
int x=compare2(a, b);
if(x!=0){return x;}
if(a.paired() && b.paired()){
x=compare2(a.mate, b.mate);
if(x!=0){return x;}
x=compare3(a, b);
if(x!=0){return x;}
x=compare3(a.mate, b.mate);
return x;
}else{
assert(!a.paired() && !b.paired());
return compare3(a, b);
}
}
if(!a.mapped() && !b.mapped()){
int x=compare2(a.mate, b.mate);
if(x!=0){return x;}
return compare3(a.mate, b.mate);
}else if(a.mapped()){
if(a.paired()){
int x=compare2(a.mate, b.mate);
if(x!=0){return x;}
return -1;
}else{
int x=compareCross(a, b.mate);
if(x!=0){return x;}
return -1;
}
}else if(b.mapped()){
if(b.paired()){
int x=compare2(a.mate, b.mate);
if(x!=0){return x;}
return 1;
}else{
int x=compareCross(b, a.mate);
if(x!=0){return 0-x;}
return 1;
}
}else{
assert(false) : a.mapped()+", "+a.paired()+", "+b.mapped()+", "+b.paired()+", "+a.mate.mapped()+", "+b.mate.mapped();
}
//I think this is unreachable...
return compare3(a, b);
}
}
public int compare2(Read a, Read b) {//TODO: This could all be packed in a long (the ID).
if(a.mapped() && !b.mapped()){return -1;}
if(b.mapped() && !a.mapped()){return 1;}
if(a.chrom!=b.chrom){return a.chrom-b.chrom;}
if(a.strand()!=b.strand()){return a.strand()-b.strand();}
assert(!SAME_STRAND_PAIRS) : "TODO";
if(a.strand()==Shared.PLUS){
if(a.start!=b.start){return a.start-b.start;}
}else{
if(a.stop!=b.stop){return a.stop-b.stop;}
}
if(a.paired()!=b.paired()){return a.paired() ? -1 : 1;}
return 0;
}
public int compareCross(Read a, Read b) {
if(a.mapped() && !b.mapped()){return -1;}
if(b.mapped() && !a.mapped()){return 1;}
if(a.chrom!=b.chrom){return a.chrom-b.chrom;}
if(SAME_STRAND_PAIRS){
if(a.strand()!=b.strand()){
return a.strand()-b.strand();
}
}else{
if(a.strand()==b.strand()){
return a.strand()==0 ? -1 : 1;
}
}
if(a.start!=b.start){return a.start-b.start;}
if(a.paired()!=b.paired()){return a.paired() ? -1 : 1;}
return 0;
}
public int compare3(Read a, Read b){
if(a.length()!=b.length()){
return b.length()-a.length(); //Preferentially puts longer reads first
}
if(a.perfect() != b.perfect()){return a.perfect() ? -1 : 1;}
int x;
if(a.match!=null && b.match!=null){
x=compareMatchStrings(a.match, b.match);
if(x!=0){return x;}
}
assert(!SAME_STRAND_PAIRS) : "TODO";
if(a.strand()==Shared.PLUS){
if(a.start!=b.start){return a.start-b.start;} //This line should be dead code
if(a.stop!=b.stop){return a.stop-b.stop;}
}else{
if(a.stop!=b.stop){return a.stop-b.stop;} //This line should be dead code
if(a.start!=b.start){return a.start-b.start;}
}
x=compareVectors(a.quality, b.quality);
if(x!=0){return 0-x;}
// if(a.stop!=b.stop){return a.stop-b.stop;}
if(a.numericID!=b.numericID){return a.numericID>b.numericID ? 1 : -1;}
return a.id.compareTo(b.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 compareMatchStrings(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]){
boolean ad=(a[i]=='D');
boolean bd=(b[i]=='D');
boolean ai=(a[i]=='I' || a[i]=='X' || a[i]=='Y');
boolean bi=(b[i]=='I' || b[i]=='X' || b[i]=='Y');
if(ai!=bi){return ai ? 1 : -1;}
if(ad!=bd){return ad ? 1 : -1;}
}
}
return 0;
}
public static boolean SAME_STRAND_PAIRS=false;
}
|
