libStatGen Software  1
SamFileTest.cpp
1 /*
2  * Copyright (C) 2010 Regents of the University of Michigan
3  *
4  * This program is free software: you can redistribute it and/or modify
5  * it under the terms of the GNU General Public License as published by
6  * the Free Software Foundation, either version 3 of the License, or
7  * (at your option) any later version.
8  *
9  * This program is distributed in the hope that it will be useful,
10  * but WITHOUT ANY WARRANTY; without even the implied warranty of
11  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12  * GNU General Public License for more details.
13  *
14  * You should have received a copy of the GNU General Public License
15  * along with this program. If not, see <http://www.gnu.org/licenses/>.
16  */
17 
18 #include "SamFileTest.h"
19 #include "SamFile.h"
20 
21 void testSamFile()
22 {
23  SamFileHeader header;
24 
25  // Test open for read via the constructor with return.
26  SamFile samInConstructorReadDefault("testFiles/testSam.sam",
29  assert(samInConstructorReadDefault.WriteHeader(header) == false);
30  assert(samInConstructorReadDefault.ReadHeader(header) == true);
31 
32  // Test open for write via the constructor.
33  SamFile samInConstructorWrite("results/newWrite.sam", SamFile::WRITE,
35  assert(samInConstructorWrite.ReadHeader(header) == false);
36  assert(samInConstructorWrite.WriteHeader(header) == true);
37 
38  // Test open for read via the constructor
39  SamFile samInConstructorRead("testFiles/testSam.sam", SamFile::READ);
40  bool caughtException = false;
41  try
42  {
43  assert(samInConstructorRead.WriteHeader(header) == false);
44  }
45  catch (std::exception& e)
46  {
47  caughtException = true;
48  }
49  assert(caughtException);
50  assert(samInConstructorRead.ReadHeader(header) == true);
51 
52  // Test open for write via child class.
53  SamFileWriter samWriteConstructor("results/newWrite1.sam");
54  caughtException = false;
55  try
56  {
57  assert(samWriteConstructor.ReadHeader(header) == false);
58  }
59  catch (std::exception& e)
60  {
61  caughtException = true;
62  }
63  assert(caughtException);
64  assert(samWriteConstructor.WriteHeader(header) == true);
65 
66  // Test open for read via child class.
67  SamFileReader samReadConstructor("testFiles/testSam.sam");
68  caughtException = false;
69  try
70  {
71  assert(samReadConstructor.WriteHeader(header) == false);
72  }
73  catch (std::exception& e)
74  {
75  caughtException = true;
76  }
77  assert(caughtException);
78  assert(samReadConstructor.ReadHeader(header) == true);
79 }
SamFile::READ
@ READ
open for reading.
Definition: SamFile.h:40
ErrorHandler::RETURN
@ RETURN
just return failure on the error
Definition: ErrorHandler.h:31
SamFile::WRITE
@ WRITE
open for writing.
Definition: SamFile.h:41
SamFileWriter
Child class of SamFile for writing files.
Definition: SamFile.h:485
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:34
SamFile
Allows the user to easily read/write a SAM/BAM file.
Definition: SamFile.h:35
SamFileReader
Child class of SamFile for reading files.
Definition: SamFile.h:455