libStatGen Software 1
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Main.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 "ReadFiles.h"
19#include "WriteFiles.h"
20#include "ValidationTest.h"
21#include "BamIndexTest.h"
22#include "ModifyVar.h"
23#include "Modify.h"
24#include "SamFileTest.h"
25#include "TestEquals.h"
26#include "TestFilter.h"
27#include "ShiftIndels.h"
28#include "TestPileup.h"
29#include "TestPosList.h"
30#include "TestCigarHelper.h"
31#include "TestSamRecordPool.h"
32#include "TestSamCoordOutput.h"
33#include "TestSamRecordHelper.h"
34
35int main(int argc, char ** argv)
36{
37 if(argc == 1)
38 {
39 testReadSam();
40#ifdef __ZLIB_AVAILABLE__
41 testReadBam();
42 testReadBam();
43#endif
44 testAddHeaderAndTagToFile("testFiles/testSam.sam",
45 "results/addedTagToSam.bam");
46 testAddHeaderAndTagToFile("testFiles/testSam.sam",
47 "results/addedTagToSam.sam");
48// Can't read bams without zlib
49#ifdef __ZLIB_AVAILABLE__
50 testAddHeaderAndTagToFile("testFiles/testBam.bam",
51 "results/addedTagToBam.sam");
52 testAddHeaderAndTagToFile("testFiles/testBam.bam",
53 "results/addedTagToBam.bam");
54#endif
55
56 testValidateSortedRead();
57
58 testWrite();
59
60 testSamQNAME();
61 testBamRID();
62 testEmptyQual();
63
64// Can't read bams without zlib
65#ifdef __ZLIB_AVAILABLE__
66 testBamIndex();
67#endif
68
69 testModifyVar();
70 testModify();
71
72 testSamFile();
73
74 testSeqEquals();
75
76 testFilter();
77
78 testShiftIndels();
79
80 testPileup();
81
82 testPosList();
83
84 testCigarHelper();
85 testSamRecordPool();
86 testSamCoordOutput();
87 testSamRecordHelper();
88 }
89 else
90 {
91 modifyFirstBaseLong();
92 }
93}
94