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: 19 September 2010
7 // ---------------------------------------------------------------------------
8 // Integrates a number of BamTools functionalities into a single executable.
9 // ***************************************************************************
12 #include "bamtools_convert.h"
13 #include "bamtools_count.h"
14 #include "bamtools_coverage.h"
15 #include "bamtools_filter.h"
16 #include "bamtools_header.h"
17 #include "bamtools_index.h"
18 #include "bamtools_merge.h"
19 #include "bamtools_random.h"
20 #include "bamtools_sort.h"
21 #include "bamtools_split.h"
22 #include "bamtools_stats.h"
24 using namespace BamTools;
26 // ------------------------------------------
27 // bamtools subtool names
28 static const string CONVERT = "convert";
29 static const string COUNT = "count";
30 static const string COVERAGE = "coverage";
31 static const string FILTER = "filter";
32 static const string HEADER = "header";
33 static const string INDEX = "index";
34 static const string MERGE = "merge";
35 static const string RANDOM = "random";
36 static const string SORT = "sort";
37 static const string SPLIT = "split";
38 static const string STATS = "stats";
40 // ------------------------------------------
41 // bamtools help/version names
42 static const string HELP = "help";
43 static const string LONG_HELP = "--help";
44 static const string SHORT_HELP = "-h";
46 static const string VERSION = "version";
47 static const string LONG_VERSION = "--version";
48 static const string SHORT_VERSION = "-v";
50 // ------------------------------------------
51 // Subtool factory method
52 AbstractTool* CreateTool(const string& arg) {
54 // determine tool type based on arg
55 if ( arg == CONVERT ) return new ConvertTool;
56 if ( arg == COUNT ) return new CountTool;
57 if ( arg == COVERAGE ) return new CoverageTool;
58 if ( arg == FILTER ) return new FilterTool;
59 if ( arg == HEADER ) return new HeaderTool;
60 if ( arg == INDEX ) return new IndexTool;
61 if ( arg == MERGE ) return new MergeTool;
62 if ( arg == RANDOM ) return new RandomTool;
63 if ( arg == SORT ) return new SortTool;
64 if ( arg == SPLIT ) return new SplitTool;
65 if ( arg == STATS ) return new StatsTool;
71 // ------------------------------------------
73 int Help(int argc, char* argv[]) {
75 // 'bamtools help COMMAND'
78 AbstractTool* tool = CreateTool( argv[2] );
79 // if ( argv[2] == CONVERT ) tool = new ConvertTool;
80 // if ( argv[2] == COUNT ) tool = new CountTool;
81 // if ( argv[2] == COVERAGE ) tool = new CoverageTool;
82 // if ( argv[2] == FILTER ) tool = new FilterTool;
83 // if ( argv[2] == HEADER ) tool = new HeaderTool;
84 // if ( argv[2] == INDEX ) tool = new IndexTool;
85 // if ( argv[2] == MERGE ) tool = new MergeTool;
86 // if ( argv[2] == RANDOM ) tool = new RandomTool;
87 // if ( argv[2] == SORT ) tool = new SortTool;
88 // if ( argv[2] == SPLIT ) tool = new SplitTool;
89 // if ( argv[2] == STATS ) tool = new StatsTool;
91 // if tool known, print its help screen
92 if ( tool ) return tool->Help();
95 // either 'bamtools help' or unrecognized argument after 'help'
97 cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
99 cerr << "Available bamtools commands:" << endl;
100 cerr << "\tconvert Converts between BAM and a number of other formats" << endl;
101 cerr << "\tcount Prints number of alignments in BAM file(s)" << endl;
102 cerr << "\tcoverage Prints coverage statistics from the input BAM file" << endl;
103 cerr << "\tfilter Filters BAM file(s) by user-specified criteria" << endl;
104 cerr << "\theader Prints BAM header information" << endl;
105 cerr << "\tindex Generates index for BAM file" << endl;
106 cerr << "\tmerge Merge multiple BAM files into single file" << endl;
107 cerr << "\trandom Select random alignments from existing BAM file(s)" << endl;
108 cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
109 cerr << "\tsplit Splits a BAM file on user-specified property, creating a new BAM output file for each value found" << endl;
110 cerr << "\tstats Prints some basic statistics from input BAM file(s)" << endl;
112 cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
117 // ------------------------------------------
118 // Print version info
121 cout << "bamtools v0.8.xx" << endl;
122 cout << "Part of BamTools API and toolkit" << endl;
123 cout << "Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg" << endl;
124 cout << "(c) 2009-2010 Marth Lab, Biology Dept., Boston College" << endl;
129 // ------------------------------------------
130 // toolkit entry point
131 int main(int argc, char* argv[]) {
134 if ( (argc == 1) ) return Help(argc, argv);
136 // 'bamtools help', 'bamtools --help', or 'bamtools -h'
137 if ( (argv[1] == HELP) || (argv[1] == LONG_HELP) || (argv[1] == SHORT_HELP) ) return Help(argc, argv);
139 // 'bamtools version', 'bamtools --version', or 'bamtools -v'
140 if ( (argv[1] == VERSION) || (argv[1] == LONG_VERSION) || (argv[1] == SHORT_VERSION) ) return Version();
142 // determine desired sub-tool
143 AbstractTool* tool = CreateTool( argv[1] );
144 // if ( argv[1] == CONVERT ) tool = new ConvertTool;
145 // if ( argv[1] == COUNT ) tool = new CountTool;
146 // if ( argv[1] == COVERAGE ) tool = new CoverageTool;
147 // if ( argv[1] == FILTER ) tool = new FilterTool;
148 // if ( argv[1] == HEADER ) tool = new HeaderTool;
149 // if ( argv[1] == INDEX ) tool = new IndexTool;
150 // if ( argv[1] == MERGE ) tool = new MergeTool;
151 // if ( argv[1] == RANDOM ) tool = new RandomTool;
152 // if ( argv[1] == SORT ) tool = new SortTool;
153 // if ( argv[1] == SPLIT ) tool = new SplitTool;
154 // if ( argv[1] == STATS ) tool = new StatsTool;
156 // if found, run tool
157 if ( tool ) return tool->Run(argc, argv);
158 // no match found, show help
159 else return Help(argc, argv);