src/toolkit/bamtools_coverage.cpp

   1 // ***************************************************************************
   2 // bamtools_coverage.cpp (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 16 September 2010
   7 // ---------------------------------------------------------------------------
   8 // Prints coverage data for a single BAM file
   9 // ***************************************************************************
  10
  11 #include <iostream>
  12 #include <fstream>
  13 #include <string>
  14 #include <vector>
  15 #include "bamtools_coverage.h"
  16 #include "bamtools_options.h"
  17 #include "bamtools_pileup_engine.h"
  18 #include "BamReader.h"
  19 using namespace std;
  20 using namespace BamTools;
  21
  22 namespace BamTools {
  23
  24 // ---------------------------------------------
  25 // CoverageVisitor implementation
  26
  27 class CoverageVisitor : public PileupVisitor {
  28
  29     public:
  30         CoverageVisitor(const RefVector& references, ostream* out)
  31             : PileupVisitor()
  32             , m_references(references)
  33             , m_out(out)
  34         { }
  35         ~CoverageVisitor(void) { }
  36
  37     // PileupVisitor interface implementation
  38     public:
  39 //         void Visit(const int& refId, const int& position, const vector<BamAlignment>& alignments) {
  40         void Visit(const PileupPosition& pileupData) {
  41             // -----------------------------------------
  42             // print coverage results ( tab-delimited )
  43             // <refName> <0-based pos> <number of alleles>
  44 //             *m_out << m_references[refId].RefName << "\t" << position << "\t" << alignments.size() << endl;
  45             *m_out << m_references[pileupData.RefId].RefName << "\t"
  46                    << pileupData.Position << "\t"
  47                    << pileupData.PileupAlignments.size() << endl;
  48         }
  49
  50     private:
  51         RefVector m_references;
  52         ostream*  m_out;
  53 };
  54
  55 } // namespace BamTools
  56
  57 // ---------------------------------------------
  58 // CoverageSettings implementation
  59
  60 struct CoverageTool::CoverageSettings {
  61
  62     // flags
  63     bool HasInputFile;
  64     bool HasOutputFile;
  65
  66     // filenames
  67     string InputBamFilename;
  68     string OutputFilename;
  69
  70     // constructor
  71     CoverageSettings(void)
  72         : HasInputFile(false)
  73         , HasOutputFile(false)
  74         , InputBamFilename(Options::StandardIn())
  75         , OutputFilename(Options::StandardOut())
  76     { }
  77 };
  78
  79 // ---------------------------------------------
  80 // CoverageToolPrivate implementation
  81
  82 struct CoverageTool::CoverageToolPrivate {
  83
  84     // ctor & dtor
  85     public:
  86         CoverageToolPrivate(CoverageTool::CoverageSettings* settings);
  87         ~CoverageToolPrivate(void);
  88
  89     // interface
  90     public:
  91         bool Run(void);
  92
  93     // data members
  94     private:
  95         CoverageTool::CoverageSettings* m_settings;
  96         ostream m_out;
  97         RefVector m_references;
  98 };
  99
 100 CoverageTool::CoverageToolPrivate::CoverageToolPrivate(CoverageTool::CoverageSettings* settings)
 101     : m_settings(settings)
 102     , m_out(cout.rdbuf()) // default output to cout
 103 { }
 104
 105 CoverageTool::CoverageToolPrivate::~CoverageToolPrivate(void) { }
 106
 107 bool CoverageTool::CoverageToolPrivate::Run(void) {
 108
 109     // if output filename given
 110     ofstream outFile;
 111     if ( m_settings->HasOutputFile ) {
 112
 113         // open output file stream
 114         outFile.open(m_settings->OutputFilename.c_str());
 115         if ( !outFile ) {
 116             cerr << "Could not open " << m_settings->OutputFilename << " for output." << endl;
 117             return false;
 118         }
 119
 120         // set m_out to file's streambuf
 121         m_out.rdbuf(outFile.rdbuf());
 122     }
 123
 124     //open our BAM reader
 125     BamReader reader;
 126     if (!reader.Open(m_settings->InputBamFilename)) {
 127         cerr << "Could not open " << m_settings->InputBamFilename << " for reading." << endl;
 128         return false;
 129     }
 130     m_references = reader.GetReferenceData();
 131
 132     // set up our output 'visitor'
 133     CoverageVisitor* cv = new CoverageVisitor(m_references, &m_out);
 134
 135     // set up pileup engine with 'visitor'
 136     PileupEngine pileup;
 137     pileup.AddVisitor(cv);
 138
 139     // process input data
 140     BamAlignment al;
 141     while ( reader.GetNextAlignment(al) )
 142         pileup.AddAlignment(al);
 143
 144     // clean up
 145     reader.Close();
 146     if ( m_settings->HasOutputFile ) outFile.close();
 147     delete cv;
 148     cv = 0;
 149
 150     // return success
 151     return true;
 152 }
 153
 154 // ---------------------------------------------
 155 // CoverageTool implementation
 156
 157 CoverageTool::CoverageTool(void)
 158     : AbstractTool()
 159     , m_settings(new CoverageSettings)
 160     , m_impl(0)
 161 {
 162     // set program details
 163     Options::SetProgramInfo("bamtools coverage", "prints coverage data for a single BAM file", "[-in <filename>] [-out <filename>]");
 164
 165     // set up options
 166     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
 167     Options::AddValueOption("-in",  "BAM filename", "the input BAM file", "", m_settings->HasInputFile,  m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
 168     Options::AddValueOption("-out", "filename",     "the output file",    "", m_settings->HasOutputFile, m_settings->OutputFilename,   IO_Opts, Options::StandardOut());
 169 }
 170
 171 CoverageTool::~CoverageTool(void) {
 172     delete m_settings;
 173     m_settings = 0;
 174
 175     delete m_impl;
 176     m_impl = 0;
 177 }
 178
 179 int CoverageTool::Help(void) {
 180     Options::DisplayHelp();
 181     return 0;
 182 }
 183
 184 int CoverageTool::Run(int argc, char* argv[]) {
 185
 186     // parse command line arguments
 187     Options::Parse(argc, argv, 1);
 188
 189     // run internal ConvertTool implementation, return success/fail
 190     m_impl = new CoverageToolPrivate(m_settings);
 191
 192     if ( m_impl->Run() )
 193         return 0;
 194     else
 195         return 1;
 196 }