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: 7 April 2011
   7 // ---------------------------------------------------------------------------
   8 // Prints coverage data for a single BAM file
   9 // ***************************************************************************
  10
  11 #include "bamtools_coverage.h"
  12
  13 #include <api/BamReader.h>
  14 #include <utils/bamtools_options.h>
  15 #include <utils/bamtools_pileup_engine.h>
  16 using namespace BamTools;
  17
  18 #include <iostream>
  19 #include <fstream>
  20 #include <string>
  21 #include <vector>
  22 using namespace std;
  23
  24 namespace BamTools {
  25
  26 // ---------------------------------------------
  27 // CoverageVisitor implementation
  28
  29 class CoverageVisitor : public PileupVisitor {
  30
  31     public:
  32         CoverageVisitor(const RefVector& references, ostream* out)
  33             : PileupVisitor()
  34             , m_references(references)
  35             , m_out(out)
  36         { }
  37         ~CoverageVisitor(void) { }
  38
  39     // PileupVisitor interface implementation
  40     public:
  41         // prints coverage results ( tab-delimited )
  42         void Visit(const PileupPosition& pileupData) {
  43             *m_out << m_references[pileupData.RefId].RefName << "\t"
  44                    << pileupData.Position << "\t"
  45                    << pileupData.PileupAlignments.size() << endl;
  46         }
  47
  48     private:
  49         RefVector m_references;
  50         ostream*  m_out;
  51 };
  52
  53 } // namespace BamTools
  54
  55 // ---------------------------------------------
  56 // CoverageSettings implementation
  57
  58 struct CoverageTool::CoverageSettings {
  59
  60     // flags
  61     bool HasInputFile;
  62     bool HasOutputFile;
  63
  64     // filenames
  65     string InputBamFilename;
  66     string OutputFilename;
  67
  68     // constructor
  69     CoverageSettings(void)
  70         : HasInputFile(false)
  71         , HasOutputFile(false)
  72         , InputBamFilename(Options::StandardIn())
  73         , OutputFilename(Options::StandardOut())
  74     { }
  75 };
  76
  77 // ---------------------------------------------
  78 // CoverageToolPrivate implementation
  79
  80 struct CoverageTool::CoverageToolPrivate {
  81
  82     // ctor & dtor
  83     public:
  84         CoverageToolPrivate(CoverageTool::CoverageSettings* settings)
  85             : m_settings(settings)
  86             , m_out(cout.rdbuf())
  87         { }
  88
  89         ~CoverageToolPrivate(void) { }
  90
  91     // interface
  92     public:
  93         bool Run(void);
  94
  95     // data members
  96     private:
  97         CoverageTool::CoverageSettings* m_settings;
  98         ostream m_out;
  99         RefVector m_references;
 100 };
 101
 102 bool CoverageTool::CoverageToolPrivate::Run(void) {
 103
 104     // if output filename given
 105     ofstream outFile;
 106     if ( m_settings->HasOutputFile ) {
 107
 108         // open output file stream
 109         outFile.open(m_settings->OutputFilename.c_str());
 110         if ( !outFile ) {
 111             cerr << "bamtools coverage ERROR: could not open " << m_settings->OutputFilename
 112                  << " for output" << endl;
 113             return false;
 114         }
 115
 116         // set m_out to file's streambuf
 117         m_out.rdbuf(outFile.rdbuf());
 118     }
 119
 120     //open our BAM reader
 121     BamReader reader;
 122     if ( !reader.Open(m_settings->InputBamFilename) ) {
 123         cerr << "bamtools coverage ERROR: could not open input BAM file: " << m_settings->InputBamFilename << endl;
 124         return false;
 125     }
 126
 127     // retrieve references
 128     m_references = reader.GetReferenceData();
 129
 130     // set up our output 'visitor'
 131     CoverageVisitor* cv = new CoverageVisitor(m_references, &m_out);
 132
 133     // set up pileup engine with 'visitor'
 134     PileupEngine pileup;
 135     pileup.AddVisitor(cv);
 136
 137     // process input data
 138     BamAlignment al;
 139     while ( reader.GetNextAlignment(al) )
 140         pileup.AddAlignment(al);
 141
 142     // clean up
 143     reader.Close();
 144     if ( m_settings->HasOutputFile )
 145         outFile.close();
 146     delete cv;
 147     cv = 0;
 148
 149     // return success
 150     return true;
 151 }
 152
 153 // ---------------------------------------------
 154 // CoverageTool implementation
 155
 156 CoverageTool::CoverageTool(void)
 157     : AbstractTool()
 158     , m_settings(new CoverageSettings)
 159     , m_impl(0)
 160 {
 161     // set program details
 162     Options::SetProgramInfo("bamtools coverage", "prints coverage data for a single BAM file", "[-in <filename>] [-out <filename>]");
 163
 164     // set up options
 165     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
 166     Options::AddValueOption("-in",  "BAM filename", "the input BAM file", "", m_settings->HasInputFile,  m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
 167     Options::AddValueOption("-out", "filename",     "the output file",    "", m_settings->HasOutputFile, m_settings->OutputFilename,   IO_Opts, Options::StandardOut());
 168 }
 169
 170 CoverageTool::~CoverageTool(void) {
 171
 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     // initialize CoverageTool with settings
 190     m_impl = new CoverageToolPrivate(m_settings);
 191
 192     // run CoverageTool, return success/fail
 193     if ( m_impl->Run() )
 194         return 0;
 195     else
 196         return 1;
 197 }