src/toolkit/bamtools_resolve.cpp

   1 // ***************************************************************************
   2 // bamtools_resolve.cpp (c) 2011
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 7 April 2011
   7 // ---------------------------------------------------------------------------
   8 // Resolves paired-end reads (marking the IsProperPair flag as needed)
   9 // ***************************************************************************
  10
  11 #include "bamtools_resolve.h"
  12
  13 #include <api/BamReader.h>
  14 #include <api/BamWriter.h>
  15 #include <utils/bamtools_options.h>
  16 #include <utils/bamtools_utilities.h>
  17 using namespace BamTools;
  18
  19 #include <iostream>
  20 #include <string>
  21 using namespace std;
  22
  23 // ---------------------------------------------
  24 // ResolveSettings implementation
  25
  26 struct ResolveTool::ResolveSettings {
  27
  28     // flags
  29     bool HasInput;
  30     bool HasOutput;
  31     bool IsForceCompression;
  32
  33     // filenames
  34     string InputFilename;
  35     string OutputFilename;
  36
  37     // constructor
  38     ResolveSettings(void)
  39         : HasInput(false)
  40         , HasOutput(false)
  41         , IsForceCompression(false)
  42         , InputFilename(Options::StandardIn())
  43         , OutputFilename(Options::StandardOut())
  44     { }
  45 };
  46
  47 // ---------------------------------------------
  48 // ResolveToolPrivate implementation
  49
  50 struct ResolveTool::ResolveToolPrivate {
  51
  52     // ctor & dtor
  53     public:
  54         ResolveToolPrivate(ResolveTool::ResolveSettings* settings)
  55             : m_settings(settings)
  56         { }
  57
  58         ~ResolveToolPrivate(void) { }
  59
  60     // 'public' interface
  61     public:
  62         bool Run(void);
  63
  64     // internal methods
  65     private:
  66
  67     // data members
  68     private:
  69         ResolveTool::ResolveSettings* m_settings;
  70 };
  71
  72 bool ResolveTool::ResolveToolPrivate::Run(void) {
  73     cerr << "Resoling BAM file..." << endl;
  74     return true;
  75 }
  76
  77 // ---------------------------------------------
  78 // ResolveTool implementation
  79
  80 ResolveTool::ResolveTool(void)
  81     : AbstractTool()
  82     , m_settings(new ResolveSettings)
  83     , m_impl(0)
  84 {
  85     // set program details
  86     Options::SetProgramInfo("bamtools resolve", "resolves paired-end reads (marking the IsProperPair flag as needed)", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [resolveOptions]");
  87
  88     // set up options
  89     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
  90     Options::AddValueOption("-in",  "BAM filename", "the input BAM file",  "", m_settings->HasInput,  m_settings->InputFilename,  IO_Opts, Options::StandardIn());
  91     Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
  92     Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
  93 }
  94
  95 ResolveTool::~ResolveTool(void) {
  96
  97     delete m_settings;
  98     m_settings = 0;
  99
 100     delete m_impl;
 101     m_impl = 0;
 102 }
 103
 104 int ResolveTool::Help(void) {
 105     Options::DisplayHelp();
 106     return 0;
 107 }
 108
 109 int ResolveTool::Run(int argc, char* argv[]) {
 110
 111     // parse command line arguments
 112     Options::Parse(argc, argv, 1);
 113
 114     // initialize ResolveTool
 115     m_impl = new ResolveToolPrivate(m_settings);
 116
 117     // run ResolveTool, return success/failure
 118     if ( m_impl->Run() ) return 0;
 119     else return 1;
 120 }