libStatGen Software 1
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TestSamRecordHelper.cpp
1/*
2 * Copyright (C) 2012 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 "TestSamRecordHelper.h"
19#include "TestValidate.h"
20#include "SamRecordHelper.h"
21#include <assert.h>
22
23void testSamRecordHelper()
24{
25 // Call generic test.
26 SamRecordHelperTest::testSamRecordHelper("testFiles/testSam.sam");
27 // SamRecordHelperTest::testSamRecordHelper("testFiles/testBam.bam");
28}
29
30
31void SamRecordHelperTest::testSamRecordHelper(const char* fileName)
32{
33 SamFile inSam;
34 assert(inSam.OpenForRead(fileName));
35 SamFileHeader samHeader;
36 assert(inSam.ReadHeader(samHeader));
37 validateHeader(samHeader);
38
39 SamRecord samRecord;
40 assert(inSam.ReadRecord(samHeader, samRecord) == true);
41 validateRead1(samRecord);
42
43 // Validate the entire sequence matches.
44 assert(SamRecordHelper::checkSequence(samRecord,
45 TestValidate::READ1_POS,
46 TestValidate::READ1_SEQ.c_str()) == 0);
47
48 // The read start position is 1010.
49 // The sequence is CCGAA.
50 assert(SamRecordHelper::checkSequence(samRecord, 1010, "CCGAA") == 0);
51
52 // Test not matching.
53 assert(SamRecordHelper::checkSequence(samRecord, 1010, "NNNNN") == -1);
54
55 // Test match, but not at the start.
56 assert(SamRecordHelper::checkSequence(samRecord, 1011, "CGA") == 1);
57
58 // Test match not at the start, but to the end.
59 assert(SamRecordHelper::checkSequence(samRecord, 1011, "CGAA") == 1);
60
61 // Test run over the end.
62 assert(SamRecordHelper::checkSequence(samRecord, 1011, "CGAAC") == -1);
63
64}
65
66
This class allows a user to get/set the fields in a SAM/BAM Header.
Allows the user to easily read/write a SAM/BAM file.
Definition SamFile.h:36
bool ReadHeader(SamFileHeader &header)
Reads the header section from the file and stores it in the passed in header.
Definition SamFile.cpp:450
bool ReadRecord(SamFileHeader &header, SamRecord &record)
Reads the next record from the file & stores it in the passed in record.
Definition SamFile.cpp:514
bool OpenForRead(const char *filename, SamFileHeader *header=NULL)
Open a sam/bam file for reading with the specified filename, determing the type of file and SAM/BAM b...
Definition SamFile.cpp:93
static int checkSequence(SamRecord &record, int32_t pos0Based, const char *sequence)
Helper method that checks if the record's read sequence starting at the specified 0-based reference p...
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition SamRecord.h:52