// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 26 May 2010
+// Last modified: 2 June 2010
// ---------------------------------------------------------------------------
// Integrates a number of BamTools functionalities into a single executable.
// ***************************************************************************
#include <iostream>
// BamTools includes
+#include "bamtools_convert.h"
+#include "bamtools_count.h"
#include "bamtools_coverage.h"
-#include "bamtools_dump.h"
+#include "bamtools_filter.h"
#include "bamtools_header.h"
#include "bamtools_index.h"
#include "bamtools_merge.h"
// ------------------------------------------
// bamtools subtool names
+static const string CONVERT = "convert";
+static const string COUNT = "count";
static const string COVERAGE = "coverage";
-static const string DUMP = "dump"; // <-- do we even want to keep this? I think 'bamtools sam' will be more useful anyway
- // nobody's going to want what was essentially an early, bloated, debugging output
+static const string FILTER = "filter";
static const string HEADER = "header";
static const string INDEX = "index";
static const string MERGE = "merge";
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) {
- if ( argv[2] == COVERAGE) return BamCoverageHelp();
- if ( argv[2] == DUMP ) return BamDumpHelp(); // keep?
- if ( argv[2] == HEADER ) return BamHeaderHelp();
- if ( argv[2] == INDEX ) return BamIndexHelp();
- if ( argv[2] == MERGE ) return BamMergeHelp();
- if ( argv[2] == SAM ) return BamSamHelp();
- if ( argv[2] == SORT ) return BamSortHelp();
- if ( argv[2] == STATS ) return BamStatsHelp();
+
+ 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();
}
-
+
// 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 << "\tcoverage\tPrints coverage statistics from the input BAM file" << endl;
- cerr << "\tdump\t\tDump BAM file contents to text output" << endl; // keep?
- cerr << "\theader\t\tPrints BAM header information" << endl;
- cerr << "\tindex\t\tGenerates index for BAM file" << endl;
- cerr << "\tmerge\t\tMerge multiple BAM files into single file" << endl;
- cerr << "\tsam\t\tPrints the BAM file in SAM (text) format" << endl;
- cerr << "\tsort\t\tSorts the BAM file according to some criteria" << endl;
- cerr << "\tstats\t\tPrints some basic statistics from the input BAM file" << 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;
}
+// ------------------------------------------
+// Print version info
int Version(void) {
cout << endl;
- cout << "bamtools v0.x.xx" << 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;
return 0;
}
+// ------------------------------------------
+// toolkit entry point
int main(int argc, char* argv[]) {
// just 'bamtools'
// 'bamtools version', 'bamtools --version', or 'bamtools -v'
if ( (argv[1] == VERSION) || (argv[1] == LONG_VERSION) || (argv[1] == SHORT_VERSION) ) return Version();
- // run desired sub-tool
- if ( argv[1] == COVERAGE ) return RunBamCoverage(argc, argv);
- if ( argv[1] == DUMP ) return RunBamDump(argc, argv); // keep?
- if ( argv[1] == HEADER ) return RunBamHeader(argc, argv);
- if ( argv[1] == INDEX ) return RunBamIndex(argc, argv);
- if ( argv[1] == MERGE ) return RunBamMerge(argc, argv);
- if ( argv[1] == SAM ) return RunBamSam(argc, argv);
- if ( argv[1] == SORT ) return RunBamSort(argc, argv);
- if ( argv[1] == STATS ) return RunBamStats(argc, argv);
+ // 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;
- // unrecognized 2nd argument, print help
- return Help(argc, argv);
+ // 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