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
|
package tracker;
import java.util.LinkedHashMap;
import java.util.Map.Entry;
import fileIO.ByteFile;
import fileIO.ReadWrite;
import shared.LineParser1;
import shared.Tools;
public class SealStats {
// #File NYUTS.fq.gz
// #Total 54848862 8282178162
// #Matched 936762 1.70790%
// #Name Reads ReadsPct Bases BasesPct
// NYUTS 914178 1.66672% 138040878 1.66672%
public SealStats(String fname_) {
fname=fname_;
load(fname);
}
void load(String fname) {
ByteFile bf=ByteFile.makeByteFile1(fname, true);
LineParser1 lp=new LineParser1('\t');
for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()) {
lp.set(line);
if(Tools.startsWith(line, '#')) {//Header
if(lp.startsWith("#File")) {
fname=lp.parseString(1);
}else if(lp.startsWith("#Total")) {
totalReads=lp.parseLong(1);
totalBases=lp.parseLong(2);
}else if(lp.startsWith("#Matched")) {
matchedReads=lp.parseLong(1);
}
}else {
String name=lp.parseString(0);
long reads=lp.parseLong(1);
long bases=lp.parseLong(3);
SealStatsLine ssl=map.get(name);
assert(ssl==null);
ssl=new SealStatsLine(name, reads, bases);
matchedBases+=bases; //Since that is not reported earlier
map.put(name, ssl);
}
}
bf.close();
}
public SealStatsLine countNonmatching(String name) {
SealStatsLine sum=new SealStatsLine("!"+name, 0, 0);
for(Entry<String, SealStatsLine> e : map.entrySet()) {
String key=e.getKey();
if(!key.equals(name)) {
SealStatsLine ssl=e.getValue();
sum.add(ssl);
}
}
return sum;
}
public SealStatsLine countNonprimary(String name) {
SealStatsLine primary=primary();
return countNonmatching(primary.name);
}
public SealStatsLine primary() {
SealStatsLine primary=null;
for(Entry<String, SealStatsLine> e : map.entrySet()) {
SealStatsLine ssl=e.getValue();
if(primary==null || ssl.compareTo(primary)>0) {primary=ssl;}
}
return primary;
}
public String fnamePrefix() {
return ReadWrite.stripToCore(fname);
}
public static class SealStatsLine implements Comparable<SealStatsLine> {
public SealStatsLine(String name_, long reads_, long bases_) {
name=name_;
reads=reads_;
bases=bases_;
}
public void add(SealStatsLine ssl) {
reads+=ssl.reads;
bases+=ssl.bases;
}
@Override
public int compareTo(SealStatsLine o) {
if(reads!=o.reads) {return reads>o.reads ? 1 : -1;}
if(bases!=o.bases) {return bases>o.bases ? 1 : -1;}
return name.compareTo(o.name);
}
@Override
public boolean equals(Object o) {return equals((SealStatsLine)o);}
public boolean equals(SealStatsLine o) {return name.equals(o.name);}
public String name;
public long reads;
public long bases;
}
public String fname;
public long totalReads, totalBases;
public long matchedReads, matchedBases;
public LinkedHashMap<String, SealStatsLine> map=new LinkedHashMap<String, SealStatsLine>();
}
|
