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
|
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.fastq;
import java.io.InputStream;
import java.io.IOException;
import java.net.URL;
/**
* Unit test for SolexaFastqReader.
*/
public final class SolexaFastqReaderTest
extends AbstractFastqReaderTest
{
/** {@inheritDoc} */
protected Fastq createFastq()
{
return new FastqBuilder()
.withDescription("description")
.withSequence("sequence")
.withQuality("quality_")
.withVariant(FastqVariant.FASTQ_SOLEXA)
.build();
}
/** {@inheritDoc} */
protected FastqReader createFastqReader()
{
return new SolexaFastqReader();
}
/** {@inheritDoc} */
protected FastqWriter createFastqWriter()
{
return new SolexaFastqWriter();
}
public void testValidateDescription() throws Exception
{
SolexaFastqReader reader = new SolexaFastqReader();
URL invalidDescription = getClass().getResource("solexa-invalid-description.fastq");
try
{
reader.read(invalidDescription);
fail("read(invalidDescription) expected IOException");
}
catch (IOException e)
{
assertTrue(e.getMessage().contains("description must begin with a '@' character"));
}
}
public void testValidateRepeatDescription() throws Exception
{
SolexaFastqReader reader = new SolexaFastqReader();
URL invalidRepeatDescription = getClass().getResource("solexa-invalid-repeat-description.fastq");
try
{
reader.read(invalidRepeatDescription);
fail("read(invalidRepeatDescription) expected IOException");
}
catch (IOException e)
{
assertTrue(e.getMessage().contains("repeat description must match description"));
}
}
public void testWrappingAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("wrapping_as_solexa.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(3, count);
inputStream.close();
}
public void testFullRangeAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("solexa_full_range_as_solexa.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(2, count);
inputStream.close();
}
public void testMiscDnaAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_dna_as_solexa.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(4, count);
inputStream.close();
}
public void testMiscRnaAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_rna_as_solexa.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(4, count);
inputStream.close();
}
public void testLongReadsAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("longreads_as_solexa.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(10, count);
inputStream.close();
}
}
|
