// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 21 March 2011
// ---------------------------------------------------------------------------
-// Prints coverage statistics for a single BAM file
-//
-// ** Expand to multiple??
-//
+// Prints coverage data for a single BAM file
// ***************************************************************************
+#include "bamtools_coverage.h"
+
+#include <api/BamReader.h>
+#include <utils/bamtools_options.h>
+#include <utils/bamtools_pileup_engine.h>
+using namespace BamTools;
+
#include <iostream>
+#include <fstream>
#include <string>
#include <vector>
-
-#include "bamtools_coverage.h"
-#include "bamtools_options.h"
-#include "BamReader.h"
-
using namespace std;
-using namespace BamTools;
+namespace BamTools {
+
+// ---------------------------------------------
+// CoverageVisitor implementation
+
+class CoverageVisitor : public PileupVisitor {
+
+ public:
+ CoverageVisitor(const RefVector& references, ostream* out)
+ : PileupVisitor()
+ , m_references(references)
+ , m_out(out)
+ { }
+ ~CoverageVisitor(void) { }
+
+ // PileupVisitor interface implementation
+ public:
+ // prints coverage results ( tab-delimited )
+ void Visit(const PileupPosition& pileupData) {
+ *m_out << m_references[pileupData.RefId].RefName << "\t"
+ << pileupData.Position << "\t"
+ << pileupData.PileupAlignments.size() << endl;
+ }
+
+ private:
+ RefVector m_references;
+ ostream* m_out;
+};
+
+} // namespace BamTools
+
// ---------------------------------------------
// CoverageSettings implementation
struct CoverageTool::CoverageSettings {
// flags
- bool HasInputBamFilename;
+ bool HasInputFile;
+ bool HasOutputFile;
// filenames
- std::string InputBamFilename;
+ string InputBamFilename;
+ string OutputFilename;
// constructor
CoverageSettings(void)
- : HasInputBamFilename(false)
+ : HasInputFile(false)
+ , HasOutputFile(false)
, InputBamFilename(Options::StandardIn())
+ , OutputFilename(Options::StandardOut())
{ }
};
+// ---------------------------------------------
+// CoverageToolPrivate implementation
+
+struct CoverageTool::CoverageToolPrivate {
+
+ // ctor & dtor
+ public:
+ CoverageToolPrivate(CoverageTool::CoverageSettings* settings);
+ ~CoverageToolPrivate(void);
+
+ // interface
+ public:
+ bool Run(void);
+
+ // data members
+ private:
+ CoverageTool::CoverageSettings* m_settings;
+ ostream m_out;
+ RefVector m_references;
+};
+
+CoverageTool::CoverageToolPrivate::CoverageToolPrivate(CoverageTool::CoverageSettings* settings)
+ : m_settings(settings)
+ , m_out(cout.rdbuf()) // default output to cout
+{ }
+
+CoverageTool::CoverageToolPrivate::~CoverageToolPrivate(void) { }
+
+bool CoverageTool::CoverageToolPrivate::Run(void) {
+
+ // if output filename given
+ ofstream outFile;
+ if ( m_settings->HasOutputFile ) {
+
+ // open output file stream
+ outFile.open(m_settings->OutputFilename.c_str());
+ if ( !outFile ) {
+ cerr << "bamtools coverage ERROR: could not open " << m_settings->OutputFilename
+ << " for output" << endl;
+ return false;
+ }
+
+ // set m_out to file's streambuf
+ m_out.rdbuf(outFile.rdbuf());
+ }
+
+ //open our BAM reader
+ BamReader reader;
+ if ( !reader.Open(m_settings->InputBamFilename) ) {
+ cerr << "bamtools coverage ERROR: could not open input BAM file: " << m_settings->InputBamFilename << endl;
+ return false;
+ }
+
+ // retrieve references
+ m_references = reader.GetReferenceData();
+
+ // set up our output 'visitor'
+ CoverageVisitor* cv = new CoverageVisitor(m_references, &m_out);
+
+ // set up pileup engine with 'visitor'
+ PileupEngine pileup;
+ pileup.AddVisitor(cv);
+
+ // process input data
+ BamAlignment al;
+ while ( reader.GetNextAlignment(al) )
+ pileup.AddAlignment(al);
+
+ // clean up
+ reader.Close();
+ if ( m_settings->HasOutputFile )
+ outFile.close();
+ delete cv;
+ cv = 0;
+
+ // return success
+ return true;
+}
+
// ---------------------------------------------
// CoverageTool implementation
CoverageTool::CoverageTool(void)
: AbstractTool()
, m_settings(new CoverageSettings)
+ , m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools coverage", "prints coverage stats for a BAM file", "-in <filename> ");
+ Options::SetProgramInfo("bamtools coverage", "prints coverage data for a single BAM file", "[-in <filename>] [-out <filename>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputFile, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-out", "filename", "the output file", "", m_settings->HasOutputFile, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
}
CoverageTool::~CoverageTool(void) {
delete m_settings;
m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
}
int CoverageTool::Help(void) {
// parse command line arguments
Options::Parse(argc, argv, 1);
-
- //open our BAM reader
- BamReader reader;
- reader.Open(m_settings->InputBamFilename);
-
- // generate coverage stats
- cerr << "Generating coverage stats for " << m_settings->InputBamFilename << endl;
- cerr << "FEATURE NOT YET IMPLEMENTED!" << endl;
-
- // clean & exit
- reader.Close();
- return 0;
-}
\ No newline at end of file
+
+ // run internal ConvertTool implementation, return success/fail
+ m_impl = new CoverageToolPrivate(m_settings);
+
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
+}
projects / bamtools.git / blobdiff