1 // ***************************************************************************
2 // bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 22 November 2010
7 // ---------------------------------------------------------------------------
8 // Integrates a number of BamTools functionalities into a single executable.
9 // ***************************************************************************
11 // stringify version information
12 #define BAMTOOLS_VER1_(x) #x
13 #define BAMTOOLS_VER_(x) BAMTOOLS_VER1_(x)
14 #define BAMTOOLS_VERSION BAMTOOLS_VER_(BT_VERSION)
21 #include "bamtools_convert.h"
22 #include "bamtools_count.h"
23 #include "bamtools_coverage.h"
24 #include "bamtools_filter.h"
25 #include "bamtools_header.h"
26 #include "bamtools_index.h"
27 #include "bamtools_merge.h"
28 #include "bamtools_random.h"
29 #include "bamtools_sort.h"
30 #include "bamtools_split.h"
31 #include "bamtools_stats.h"
32 #include "bamtools_version.h"
34 using namespace BamTools;
36 // bamtools subtool names
37 static const string CONVERT = "convert";
38 static const string COUNT = "count";
39 static const string COVERAGE = "coverage";
40 static const string FILTER = "filter";
41 static const string HEADER = "header";
42 static const string INDEX = "index";
43 static const string MERGE = "merge";
44 static const string RANDOM = "random";
45 static const string SORT = "sort";
46 static const string SPLIT = "split";
47 static const string STATS = "stats";
49 // bamtools help/version constants
50 static const string HELP = "help";
51 static const string LONG_HELP = "--help";
52 static const string SHORT_HELP = "-h";
53 static const string VERSION = "version";
54 static const string LONG_VERSION = "--version";
55 static const string SHORT_VERSION = "-v";
57 // determine if string is a help constant
58 static bool IsHelp(char* str) {
59 return ( str == HELP ||
64 // determine if string is a version constant
65 static bool IsVersion(char* str) {
66 return ( str == VERSION ||
67 str == LONG_VERSION ||
68 str == SHORT_VERSION );
71 // subtool factory method
72 AbstractTool* CreateTool(const string& arg) {
74 // determine tool type based on arg
75 if ( arg == CONVERT ) return new ConvertTool;
76 if ( arg == COUNT ) return new CountTool;
77 if ( arg == COVERAGE ) return new CoverageTool;
78 if ( arg == FILTER ) return new FilterTool;
79 if ( arg == HEADER ) return new HeaderTool;
80 if ( arg == INDEX ) return new IndexTool;
81 if ( arg == MERGE ) return new MergeTool;
82 if ( arg == RANDOM ) return new RandomTool;
83 if ( arg == SORT ) return new SortTool;
84 if ( arg == SPLIT ) return new SplitTool;
85 if ( arg == STATS ) return new StatsTool;
92 int Help(int argc, char* argv[]) {
94 // check for 'bamtools help COMMAND' to print tool-specific help message
97 // determine desired sub-tool
98 AbstractTool* tool = CreateTool( argv[2] );
100 // if tool known, print its help screen
101 if ( tool ) return tool->Help();
104 // print general BamTools help message
106 cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
108 cerr << "Available bamtools commands:" << endl;
109 cerr << "\tconvert Converts between BAM and a number of other formats" << endl;
110 cerr << "\tcount Prints number of alignments in BAM file(s)" << endl;
111 cerr << "\tcoverage Prints coverage statistics from the input BAM file" << endl;
112 cerr << "\tfilter Filters BAM file(s) by user-specified criteria" << endl;
113 cerr << "\theader Prints BAM header information" << endl;
114 cerr << "\tindex Generates index for BAM file" << endl;
115 cerr << "\tmerge Merge multiple BAM files into single file" << endl;
116 cerr << "\trandom Select random alignments from existing BAM file(s)" << endl;
117 cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
118 cerr << "\tsplit Splits a BAM file on user-specified property, creating a new BAM output file for each value found" << endl;
119 cerr << "\tstats Prints some basic statistics from input BAM file(s)" << endl;
121 cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
126 // print version info
129 stringstream versionStream("");
130 versionStream << BAMTOOLS_VERSION_MAJOR << "."
131 << BAMTOOLS_VERSION_MINOR << "."
132 << BAMTOOLS_VERSION_BUILD;
135 cout << "bamtools " << versionStream.str() << endl;
136 cout << "Part of BamTools API and toolkit" << endl;
137 cout << "Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg" << endl;
138 cout << "(c) 2009-2010 Marth Lab, Biology Dept., Boston College" << endl;
143 // toolkit entry point
144 int main(int argc, char* argv[]) {
147 if ( (argc == 1) ) return Help(argc, argv);
149 // 'bamtools help', 'bamtools --help', or 'bamtools -h'
150 if ( IsHelp(argv[1]) ) return Help(argc, argv);
152 // 'bamtools version', 'bamtools --version', or 'bamtools -v'
153 if ( IsVersion(argv[1]) ) return Version();
155 // determine desired sub-tool
156 AbstractTool* tool = CreateTool( argv[1] );
158 // if found, run tool... otherwise show help
159 if ( tool ) return tool->Run(argc, argv);
160 else return Help(argc, argv);