#include <iostream>
// BamTools includes
+#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"
// ------------------------------------------
// 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";
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;
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;
// 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;