// ***************************************************************************
-// bamtools.cpp (c) 2010 Erik Garrison
+// bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
+// Last modified: 2 June 2010
+// ---------------------------------------------------------------------------
// Integrates a number of BamTools functionalities into a single executable.
// ***************************************************************************
// Std C/C++ includes
-#include <cstdlib>
#include <iostream>
-#include <string>
-#include <boost/algorithm/string.hpp>
-using namespace std;
// BamTools includes
-#include "BamReader.h"
-#include "BamWriter.h"
-#include "BamMultiReader.h"
-using namespace BamTools;
-
-void usageSummary() {
- cerr << "usage: bamtools <command> [options]" << endl
- << "actions:" << endl
- << " index <bam file>" << endl
- << " merge <merged BAM file> [<BAM file> <BAM file> ...]" << endl
- << " dump [<BAM file> <BAM file> ...]" << endl;
- //<< " trim <input BAM file> <input BAM index file> <output BAM file> <reference name> <leftBound> <rightBound>" << endl;
-}
-
-
-void BamMerge(string outputFilename, vector<string> filenames) {
-
- BamMultiReader reader;
+#include "bamtools_convert.h"
+#include "bamtools_count.h"
+#include "bamtools_coverage.h"
+#include "bamtools_filter.h"
+#include "bamtools_header.h"
+#include "bamtools_index.h"
+#include "bamtools_merge.h"
+#include "bamtools_sam.h"
+#include "bamtools_sort.h"
+#include "bamtools_stats.h"
- reader.Open(filenames);
-
- string mergedHeader = reader.GetHeaderText();
-
- RefVector references = reader.GetReferenceData();
-
- // open BamWriter
- BamWriter writer;
- writer.Open( outputFilename.c_str(), mergedHeader, references);
+using namespace std;
+using namespace BamTools;
- BamAlignment bAlignment;
- while (reader.GetNextAlignment(bAlignment)) {
- // write to output file
- writer.SaveAlignment(bAlignment);
+// ------------------------------------------
+// bamtools subtool names
+static const string CONVERT = "convert";
+static const string COUNT = "count";
+static const string COVERAGE = "coverage";
+static const string FILTER = "filter";
+static const string HEADER = "header";
+static const string INDEX = "index";
+static const string MERGE = "merge";
+static const string SAM = "sam";
+static const string SORT = "sort";
+static const string STATS = "stats";
+
+// ------------------------------------------
+// bamtools help/version names
+static const string HELP = "help";
+static const string LONG_HELP = "--help";
+static const string SHORT_HELP = "-h";
+
+static const string VERSION = "version";
+static const string LONG_VERSION = "--version";
+static const string SHORT_VERSION = "-v";
+
+// ------------------------------------------
+// Print help info
+int Help(int argc, char* argv[]) {
+
+ // 'bamtools help COMMAND'
+ if (argc > 2) {
+
+ AbstractTool* tool(0);
+ if ( argv[2] == CONVERT ) tool = new ConvertTool;
+ if ( argv[2] == COUNT ) tool = new CountTool;
+ if ( argv[2] == COVERAGE ) tool = new CoverageTool;
+ if ( argv[2] == FILTER ) tool = new FilterTool;
+ if ( argv[2] == HEADER ) tool = new HeaderTool;
+ if ( argv[2] == INDEX ) tool = new IndexTool;
+ if ( argv[2] == MERGE ) tool = new MergeTool;
+ if ( argv[2] == SAM ) tool = new SamTool;
+ if ( argv[2] == SORT ) tool = new SortTool;
+ if ( argv[2] == STATS ) tool = new StatsTool;
+
+ // if tool known, print its help screen
+ if ( tool ) return tool->Help();
}
- // close output file
- writer.Close();
- // close input files
- reader.Close();
-
-}
-
-void BamCreateIndex(const char* inputFilename) {
-
- // open our BAM reader
- BamReader reader;
- reader.Open(inputFilename);
-
- // create index file
- reader.CreateIndex();
-
- // close our file
- reader.Close();
-
+ // either 'bamtools help' or unrecognized argument after 'help'
+ cerr << endl;
+ cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
+ cerr << endl;
+ cerr << "Available bamtools commands:" << endl;
+ cerr << "\tconvert Converts between BAM and a number of other formats" << endl;
+ cerr << "\tcount Prints number of alignments in BAM file" << endl;
+ cerr << "\tcoverage Prints coverage statistics from the input BAM file" << endl;
+ cerr << "\tfilter Filters BAM file(s) by user-specified criteria" << endl;
+ cerr << "\theader Prints BAM header information" << endl;
+ cerr << "\tindex Generates index for BAM file" << endl;
+ cerr << "\tmerge Merge multiple BAM files into single file" << endl;
+ cerr << "\tsam Prints the BAM file in SAM (text) format" << endl;
+ cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
+ cerr << "\tstats Prints some basic statistics from the input BAM file" << endl;
+ cerr << endl;
+ cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
+ cerr << endl;
+ return 0;
}
-// Spit out basic BamAlignment data
-void PrintAlignment(const BamAlignment& alignment) {
- cout << "---------------------------------" << endl;
- cout << "Name: " << alignment.Name << endl;
- cout << "Aligned to: " << alignment.RefID;
- cout << ":" << alignment.Position << endl;
- cout << endl;
-}
-
-void BamDump(vector<string> files) {
-
- BamMultiReader reader;
- reader.Open(files);
-
- BamAlignment bAlignment;
- while (reader.GetNextAlignment(bAlignment)) {
- PrintAlignment(bAlignment);
- }
-
- reader.Close();
-
+// ------------------------------------------
+// Print version info
+int Version(void) {
+ cout << endl;
+ cout << "bamtools v0.8.xx" << endl;
+ cout << "Part of BamTools API and toolkit" << endl;
+ cout << "Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg" << endl;
+ cout << "(c) 2009-2010 Marth Lab, Biology Dept., Boston College" << endl;
+ cout << endl;
+ return 0;
}
-
+// ------------------------------------------
+// toolkit entry point
int main(int argc, char* argv[]) {
- // validate argument count
- if( argc < 2 ) {
- usageSummary();
- exit(1);
- }
-
- string command = argv[1];
+ // just 'bamtools'
+ if ( (argc == 1) ) return Help(argc, argv);
- if (command == "index") {
- BamCreateIndex(argv[2]);
- } else if (command == "merge") {
- vector<string> files;
- string outputFile = argv[2];
- for (int i = 3; i<argc; ++i) {
- files.push_back(argv[i]);
- }
- BamMerge(outputFile, files);
- } else if (command == "dump") {
- vector<string> files;
- for (int i = 2; i<argc; ++i) {
- files.push_back(argv[i]);
- }
- BamDump(files);
- }
-
-
- return 0;
+ // 'bamtools help', 'bamtools --help', or 'bamtools -h'
+ if ( (argv[1] == HELP) || (argv[1] == LONG_HELP) || (argv[1] == SHORT_HELP) ) return Help(argc, argv);
+
+ // 'bamtools version', 'bamtools --version', or 'bamtools -v'
+ if ( (argv[1] == VERSION) || (argv[1] == LONG_VERSION) || (argv[1] == SHORT_VERSION) ) return Version();
+
+ // determine desired sub-tool
+ AbstractTool* tool(0);
+ if ( argv[1] == CONVERT ) tool = new ConvertTool;
+ if ( argv[1] == COUNT ) tool = new CountTool;
+ if ( argv[1] == COVERAGE ) tool = new CoverageTool;
+ if ( argv[1] == FILTER ) tool = new FilterTool;
+ if ( argv[1] == HEADER ) tool = new HeaderTool;
+ if ( argv[1] == INDEX ) tool = new IndexTool;
+ if ( argv[1] == MERGE ) tool = new MergeTool;
+ if ( argv[1] == SAM ) tool = new SamTool;
+ if ( argv[1] == SORT ) tool = new SortTool;
+ if ( argv[1] == STATS ) tool = new StatsTool;
+
+ // if found, run tool
+ if ( tool ) return tool->Run(argc, argv);
+ // no match found, show help
+ else return Help(argc, argv);
}
projects / bamtools.git / blobdiff