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
|
/**
* Copyright Copyright 2013-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* FastQC is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with FastQC; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package uk.ac.babraham.FastQC.Modules;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.InputStream;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import uk.ac.babraham.FastQC.FastQCConfig;
import uk.ac.babraham.FastQC.Sequence.Contaminant.ContaminentFinder;
public class ModuleConfig {
private static HashMap<String, Double>parameters = readParams();
private static HashMap<String, Double> readParams () {
HashMap<String, Double>params = new HashMap<String, Double>();
// Set the defaults to use if we don't have any overrides
params.put("duplication:warn",70d);
params.put("duplication:error", 50d);
params.put("kmer:warn", 2d);
params.put("kmer:error",5d);
params.put("n_content:warn",5d);
params.put("n_content:error",20d);
params.put("overrepresented:warn", 0.1);
params.put("overrepresented:error",1d);
params.put("quality_base_lower:warn",10d);
params.put("quality_base_lower:error", 5d);
params.put("quality_base_median:warn", 25d);
params.put("quality_base_median:error", 20d);
params.put("sequence:warn", 10d);
params.put("sequence:error",20d);
params.put("gc_sequence:warn",15d);
params.put("gc_sequence:error",30d);
params.put("quality_sequence:warn", 20d);
params.put("quality_sequence:error",27d);
params.put("tile:warn", 5d);
params.put("tile:error",10d);
params.put("sequence_length:warn",1d);
params.put("sequence_length:error", 1d);
params.put("adapter:warn", 5d);
params.put("adapter:error", 10d);
params.put("duplication:ignore",0d);
params.put("kmer:ignore",0d);
params.put("n_content:ignore",0d);
params.put("overrepresented:ignore",0d);
params.put("quality_base:ignore",0d);
params.put("sequence:ignore",0d);
params.put("gc_quality:ignore",0d);
params.put("quality_sequence:ignore",0d);
params.put("tile:ignore",0d);
params.put("sequence_length:ignore",0d);
params.put("adapter:ignore",0d);
// Now read the config file to see if there are updated values for any of these.
BufferedReader br;
try {
if (FastQCConfig.getInstance().limits_file == null) {
InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/limits.txt");
if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/limits.txt");
br =new BufferedReader(new InputStreamReader(rsrc));
}
else {
br=new BufferedReader(new FileReader(FastQCConfig.getInstance().limits_file));
}
String line;
while ((line = br.readLine()) != null) {
if (line.startsWith("#")) continue;
if (line.trim().length() == 0) continue;
String [] sections = line.split("\\s+");
if (sections.length != 3) {
System.err.println("Config line '"+line+"' didn't contain the 3 required sections");
}
if (!(sections[1].equals("warn") || sections[1].equals("error") || sections[1].equals("ignore"))) {
System.err.println("Second config field must be error, warn or ignore, not '"+sections[1]+"'");
continue;
}
double value;
try {
value = Double.parseDouble(sections[2]);
}
catch (NumberFormatException nfe) {
System.err.println("Value "+sections[2]+" didn't look like a number");
continue;
}
String key = sections[0]+":"+sections[1];
params.put(key, value);
}
}
catch (Exception e) {
e.printStackTrace();
}
return params;
}
public static Double getParam(String module, String level) {
if (!(level.equals("warn") || level.equals("error") || level.equals("ignore"))) {
throw new IllegalArgumentException("Level must be warn, error or ignore");
}
String key = module+":"+level;
if (! parameters.containsKey(key)) {
throw new IllegalArgumentException("No key called "+key+" in the config data");
}
return parameters.get(key);
}
}
|
