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
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
|
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program 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 General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "BamIndex.h"
#include "TestValidate.h"
#include "BamIndexTest.h"
#include <assert.h>
void testIndex(BamIndex& bamIndex)
{
#ifdef __ZLIB_AVAILABLE__
assert(bamIndex.getNumMappedReads(1) == 2);
assert(bamIndex.getNumUnMappedReads(1) == 0);
assert(bamIndex.getNumMappedReads(0) == 4);
assert(bamIndex.getNumUnMappedReads(0) == 1);
assert(bamIndex.getNumMappedReads(23) == -1);
assert(bamIndex.getNumUnMappedReads(23) == -1);
assert(bamIndex.getNumMappedReads(-1) == 0);
assert(bamIndex.getNumUnMappedReads(-1) == 2);
assert(bamIndex.getNumMappedReads(-2) == -1);
assert(bamIndex.getNumUnMappedReads(-2) == -1);
assert(bamIndex.getNumMappedReads(22) == 0);
assert(bamIndex.getNumUnMappedReads(22) == 0);
// Get the chunks for reference id 1.
Chunk testChunk;
SortedChunkList chunkList;
assert(bamIndex.getChunksForRegion(1, -1, -1, chunkList) == true);
assert(!chunkList.empty());
testChunk = chunkList.pop();
assert(chunkList.empty());
assert(testChunk.chunk_beg == 0x4e7);
assert(testChunk.chunk_end == 0x599);
// Get the chunks for reference id 0.
assert(bamIndex.getChunksForRegion(0, -1, -1, chunkList) == true);
assert(!chunkList.empty());
testChunk = chunkList.pop();
assert(chunkList.empty());
assert(testChunk.chunk_beg == 0x360);
assert(testChunk.chunk_end == 0x4e7);
// Get the chunks for reference id 2.
assert(bamIndex.getChunksForRegion(2, -1, -1, chunkList) == true);
assert(!chunkList.empty());
testChunk = chunkList.pop();
assert(chunkList.empty());
assert(testChunk.chunk_beg == 0x599);
assert(testChunk.chunk_end == 0x5ea);
// Get the chunks for reference id 3.
// There isn't one for this ref id, but still successfully read the file,
// so it should return true, but the list should be empty.
assert(bamIndex.getChunksForRegion(3, -1, -1, chunkList) == true);
assert(chunkList.empty());
// Test reading an indexed bam file.
SamFile inFile;
assert(inFile.OpenForRead("testFiles/sortedBam.bam"));
inFile.setSortedValidation(SamFile::COORDINATE);
assert(inFile.ReadBamIndex("testFiles/sortedBam.bam.bai"));
SamFileHeader samHeader;
assert(inFile.ReadHeader(samHeader));
SamRecord samRecord;
// Test getting num mapped/unmapped reads.
assert(inFile.getNumMappedReadsFromIndex(1) == 2);
assert(inFile.getNumUnMappedReadsFromIndex(1) == 0);
assert(inFile.getNumMappedReadsFromIndex(0) == 4);
assert(inFile.getNumUnMappedReadsFromIndex(0) == 1);
assert(inFile.getNumMappedReadsFromIndex(23) == -1);
assert(inFile.getNumUnMappedReadsFromIndex(23) == -1);
assert(inFile.getNumMappedReadsFromIndex(-1) == 0);
assert(inFile.getNumUnMappedReadsFromIndex(-1) == 2);
assert(inFile.getNumMappedReadsFromIndex(-2) == -1);
assert(inFile.getNumUnMappedReadsFromIndex(-2) == -1);
assert(inFile.getNumMappedReadsFromIndex(22) == 0);
assert(inFile.getNumUnMappedReadsFromIndex(22) == 0);
assert(inFile.getNumMappedReadsFromIndex("2", samHeader) == 2);
assert(inFile.getNumUnMappedReadsFromIndex("2", samHeader) == 0);
assert(inFile.getNumMappedReadsFromIndex("1", samHeader) == 4);
assert(inFile.getNumUnMappedReadsFromIndex("1", samHeader) == 1);
assert(inFile.getNumMappedReadsFromIndex("22", samHeader) == 0);
assert(inFile.getNumUnMappedReadsFromIndex("22", samHeader) == 0);
assert(inFile.getNumMappedReadsFromIndex("", samHeader) == 0);
assert(inFile.getNumUnMappedReadsFromIndex("*", samHeader) == 2);
assert(inFile.getNumMappedReadsFromIndex("unknown", samHeader) == -1);
assert(inFile.getNumUnMappedReadsFromIndex("unknown", samHeader) == -1);
assert(inFile.getNumMappedReadsFromIndex("X", samHeader) == 0);
assert(inFile.getNumUnMappedReadsFromIndex("X", samHeader) == 0);
// Set the read section saying the reads must be fully enclosed in the section.
assert(inFile.SetReadSection("1", 1010, 1011, false));
assert(inFile.ReadRecord(samHeader, samRecord) == false);
assert(inFile.SetReadSection("1", 1011, 1012, false));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead2(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
// Section -1 = Ref *: 2 records (8 & 10 from testSam.sam that is reflected
// in the validation.
assert(inFile.SetReadSection(-1));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead8(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead10(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
// Section 2 = Ref 3: 1 records (9 from testSam.sam that is reflected
// in the validation.
assert(inFile.SetReadSection(2));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead9(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
// Section 0 = Ref 1: 5 records (3, 4, 1, 2, & 6 from testSam.sam that is
// reflected in the validation.
assert(inFile.SetReadSection(0));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead3(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead4(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead1(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead2(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead6(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
// Section 1 = Ref 2: 2 records (5 & 7 from testSam.sam that is reflected
// in the validation.
assert(inFile.SetReadSection(1));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead5(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead7(samRecord);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
// Section 3 to 22 (ref 4 - 23): 0 records.
for(int i = 3; i < 23; i++)
{
assert(inFile.SetReadSection(i));
assert(inFile.ReadRecord(samHeader, samRecord) == false);
}
// Set the read section.
assert(inFile.SetReadSection("1", 1010, 1012));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead1(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 2);
assert(samRecord.getNumOverlaps(1010, 1012) == 2);
assert(samRecord.getNumOverlaps(1010, 1020) == 5);
assert(samRecord.getNumOverlaps(1010, 1011) == 1);
assert(samRecord.getNumOverlaps(1011, 1012) == 1);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead2(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 0);
assert(samRecord.getNumOverlaps(1010, 1012) == 0);
assert(samRecord.getNumOverlaps(1010, 1020) == 0);
assert(samRecord.getNumOverlaps(1010, 1011) == 0);
assert(samRecord.getNumOverlaps(1011, 1012) == 0);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
assert(inFile.SetReadSection("1", 1010, 1020));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead1(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 5);
assert(samRecord.getNumOverlaps(1010, 1012) == 2);
assert(samRecord.getNumOverlaps(1010, 1020) == 5);
assert(samRecord.getNumOverlaps(1010, 1011) == 1);
assert(samRecord.getNumOverlaps(1011, 1012) == 1);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead2(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 0);
assert(samRecord.getNumOverlaps(1010, 1012) == 0);
assert(samRecord.getNumOverlaps(1010, 1020) == 0);
assert(samRecord.getNumOverlaps(1010, 1011) == 0);
assert(samRecord.getNumOverlaps(1011, 1012) == 0);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
assert(inFile.SetReadSection("1", 1010, 1011));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead1(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 1);
assert(samRecord.getNumOverlaps(1010, 1012) == 2);
assert(samRecord.getNumOverlaps(1010, 1020) == 5);
assert(samRecord.getNumOverlaps(1010, 1011) == 1);
assert(samRecord.getNumOverlaps(1011, 1012) == 1);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
assert(inFile.SetReadSection("1", 1011, 1012));
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead1(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 1);
assert(samRecord.getNumOverlaps(1010, 1012) == 2);
assert(samRecord.getNumOverlaps(1010, 1020) == 5);
assert(samRecord.getNumOverlaps(1010, 1011) == 1);
assert(samRecord.getNumOverlaps(1011, 1012) == 1);
assert(inFile.ReadRecord(samHeader, samRecord));
validateRead2(samRecord);
assert(inFile.GetNumOverlaps(samRecord) == 0);
assert(samRecord.getNumOverlaps(1010, 1012) == 0);
assert(samRecord.getNumOverlaps(1010, 1020) == 0);
assert(samRecord.getNumOverlaps(1010, 1011) == 0);
assert(samRecord.getNumOverlaps(1011, 1012) == 0);
assert(inFile.ReadRecord(samHeader, samRecord) == false);
#endif
}
void testBamIndex()
{
// BAM indexes are compressed, so can't be tested without zlib.
#ifdef __ZLIB_AVAILABLE__
// Create a bam index.
BamIndex bamIndex;
bamIndex.readIndex("testFiles/sortedBam.bam.bai");
testIndex(bamIndex);
BamIndexFileTest test1;
bool caughtException = false;
try
{
// Try reading the bam index without specifying a
// filename and before opening a bam file.
assert(test1.ReadBamIndex() == false);
}
catch (std::exception& e)
{
caughtException = true;
assert(strcmp(e.what(), "FAIL_ORDER: Failed to read the bam Index file - the BAM file needs to be read first in order to determine the index filename.") == 0);
}
// Should have failed and thrown an exception.
assert(caughtException);
// Read the bam index with a specified name.
assert(test1.ReadBamIndex("testFiles/sortedBam.bam.bai"));
BamIndex* index = test1.getBamIndex();
assert(index != NULL);
testIndex(*index);
// Open the bam file so the index can be opened.
assert(test1.OpenForRead("testFiles/sortedBam.bam"));
// Try reading the bam index without specifying a
// filename after opening a bam file.
assert(test1.ReadBamIndex() == true);
index = test1.getBamIndex();
assert(index != NULL);
testIndex(*index);
// Open the bam file so the index can be opened.
// This time the index file does not have .bam in it.
assert(test1.OpenForRead("testFiles/sortedBam2.bam"));
// Try reading the bam index without specifying a
// filename after opening a bam file.
assert(test1.ReadBamIndex() == true);
index = test1.getBamIndex();
assert(index != NULL);
testIndex(*index);
#endif
}
|
