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
|
package artificialFastqGenerator;
import java.util.ArrayList;
/**
* An instance of this class corresponds to a read in an artificial fastq file. It has fields for its Nucleobase sequence,
* unique integer ID, the other read in the pair, its encoded quality scores, and the genotypes which actually get read (i.e.
* may contain error).
*
* Copyright (C) 2012 The Institute of Cancer Research (ICR).
*
* This file is part of ArtificialFastqGenerator v1.0.0.
*
* ArtificialFastqGenerator 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.
*
* This program 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 Public License along with this
* program. If not, see <http://www.gnu.org/licenses/>
*
* Authour's contact email: Matthew.Frampton@icr.ac.uk
*/
public class Read extends AbstractRead {
private long uniqueID;
private Read pairedEndRead;
private boolean leftPEAndNeedsWriting;
private char[] encodedQualityScores;
private char[] genotypesThatAreRead;
private String machineLaneTileXYLorR = "HWI-ST745_0097:7:1101:";
/**
* Initialise a new Read object.
*
* @param sequence - the sequence of nucleobases in this read.
* @param uniqueID - the read's unique integer ID.
* @param pairedEndRead - the other read with which this one forms a pair.
* @param leftPEAndNeedsWriting - true if the read is a left read and needs writing, else false.
* @param encodedQualityScores - the encoded quality scores for this read.
* @param genotypesThatAreRead - the genotypes that get read.
* @param xCoordinate - the read's x-coordinate.
* @param yCoordinate - the read's y-coordinate.
*/
public Read(ArrayList<Nucleobase> sequence, long uniqueID, Read pairedEndRead, boolean leftPEAndNeedsWriting, char[] encodedQualityScores,
char[] genotypesThatAreRead, int xCoordinate, int yCoordinate) {
this.sequence = sequence;
this.uniqueID = uniqueID;
this.pairedEndRead = pairedEndRead;
updateNucleobaseCoverage(this);
this.leftPEAndNeedsWriting = leftPEAndNeedsWriting;
this.encodedQualityScores = encodedQualityScores;
this.genotypesThatAreRead = genotypesThatAreRead;
this.machineLaneTileXYLorR = this.machineLaneTileXYLorR + xCoordinate + ":" + yCoordinate + "#0/";
if (leftPEAndNeedsWriting) {
this.machineLaneTileXYLorR = this.machineLaneTileXYLorR + "1";
} else {
this.machineLaneTileXYLorR = this.machineLaneTileXYLorR + "2";
}
}
/**
* Set whether the Read object is a left read and needs writing.
*
* @param trueOrFalse - true if the read is a left read and needs writing, else false.
*/
public void setLeftReadAndNeedsWriting(boolean trueOrFalse) {
leftPEAndNeedsWriting = trueOrFalse;
}
/**
* Get whether the Read object is a left read and needs writing.
*
* @return leftPEAndNeedsWriting - whether the read is a left read and needs writing (hasn't been written yet), else false.
*/
public boolean isLeftReadAndNeedsWriting() {
return leftPEAndNeedsWriting;
}
/**
* Get the read with which this read object forms a pair.
*
* @return pairedEndRead - the read with which this read forms a pair.
*/
public Read getPairedEndRead() {
return pairedEndRead;
}
/**
* Set the read with which this read object forms a pair.
*
* @param pairedEndRead - the read with which this read forms a pair.
*/
public void setPairedEndRead(Read pairedEndRead) {
this.pairedEndRead = pairedEndRead;
}
/**
* For each of the reference genome nucleobases in this read, add
* the read into the nucleobase's covering reads ArrayList.
*
* @param read - this read.
*/
public void updateNucleobaseCoverage(Read read) {
for (Nucleobase nucleobase : read.getSequence()) {
if (!nucleobase.getCoveringReads().contains(read)) {
nucleobase.addCoveringRead(read);}
else {break;}
}
}
/**
* Get the string that represents this read object.
*
* @return returnString - the string that represents this read object.
*/
public String toString() {
String returnString = new String();
if (Main.outputFormat.equals(Main.DEFAULT_OUTPUT)) {
returnString = "@" + machineLaneTileXYLorR + "\n";
for (int i=0; i<genotypesThatAreRead.length; i++) {
returnString = returnString + genotypesThatAreRead[i];
}
returnString = returnString + "\n+" + machineLaneTileXYLorR + "\n";
for (int i=0; i<encodedQualityScores.length; i++) {
returnString = returnString + encodedQualityScores[i];
}
returnString = returnString + "\n";
} else {
returnString = getDebugString() + "\n";
}
return returnString;
}
/**
* Get the debug string for this read object.
*
* @return returnString - the debug string that represents this read object.
*/
public String getDebugString() {
String returnString = "";
for (Nucleobase nucleobase : sequence) {
returnString = returnString + nucleobase.toString();
}
if (Main.outputFormat.equals(Main.DEBUG_NUCLEOBASES_PE_IDS)) {
String pairedEndStr = "null";
if (!(pairedEndRead == null)) {
pairedEndStr = String.valueOf(pairedEndRead.uniqueID);
}
returnString = returnString + " ID:" + this.uniqueID + " PE_ID:" + pairedEndStr;
}
return returnString;
}
}
|
