src/toolkit/bamtools_index.cpp

   1 // ***************************************************************************
   2 // bamtools_index.cpp (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 7 April 2011
   6 // ---------------------------------------------------------------------------
   7 // Creates a BAM index file
   8 // ***************************************************************************
   9
  10 #include "bamtools_index.h"
  11
  12 #include <api/BamReader.h>
  13 #include <utils/bamtools_options.h>
  14 using namespace BamTools;
  15
  16 #include <iostream>
  17 #include <string>
  18 using namespace std;
  19
  20 // ---------------------------------------------
  21 // IndexSettings implementation
  22
  23 struct IndexTool::IndexSettings {
  24
  25     // flags
  26     bool HasInputBamFilename;
  27     bool IsUsingBamtoolsIndex;
  28
  29     // filenames
  30     string InputBamFilename;
  31
  32     // constructor
  33     IndexSettings(void)
  34         : HasInputBamFilename(false)
  35         , IsUsingBamtoolsIndex(false)
  36         , InputBamFilename(Options::StandardIn())
  37     { }
  38 };
  39
  40 // ---------------------------------------------
  41 // IndexToolPrivate implementation
  42
  43 struct IndexTool::IndexToolPrivate {
  44
  45     // ctor & dtor
  46     public:
  47         IndexToolPrivate(IndexTool::IndexSettings* settings)
  48             : m_settings(settings)
  49         { }
  50
  51         ~IndexToolPrivate(void) { }
  52
  53     // interface
  54     public:
  55         bool Run(void);
  56
  57     // data members
  58     private:
  59         IndexTool::IndexSettings* m_settings;
  60 };
  61
  62 bool IndexTool::IndexToolPrivate::Run(void) {
  63
  64     // open our BAM reader
  65     BamReader reader;
  66     if ( !reader.Open(m_settings->InputBamFilename) ) {
  67         cerr << "bamtools index ERROR: could not open BAM file: "
  68              << m_settings->InputBamFilename << endl;
  69         return false;
  70     }
  71
  72     // create index for BAM file
  73     const BamIndex::IndexType type = ( m_settings->IsUsingBamtoolsIndex ? BamIndex::BAMTOOLS
  74                                                                         : BamIndex::STANDARD );
  75     reader.CreateIndex(type);
  76
  77     // clean & exit
  78     reader.Close();
  79     return true;
  80 }
  81
  82 // ---------------------------------------------
  83 // IndexTool implementation
  84
  85 IndexTool::IndexTool(void)
  86     : AbstractTool()
  87     , m_settings(new IndexSettings)
  88     , m_impl(0)
  89 {
  90     // set program details
  91     Options::SetProgramInfo("bamtools index", "creates index for BAM file", "[-in <filename>] [-bti]");
  92
  93     // set up options
  94     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
  95     Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
  96     Options::AddOption("-bti", "create (non-standard) BamTools index file (*.bti). Default behavior is to create standard BAM index (*.bai)", m_settings->IsUsingBamtoolsIndex, IO_Opts);
  97 }
  98
  99 IndexTool::~IndexTool(void) {
 100
 101     delete m_settings;
 102     m_settings = 0;
 103
 104     delete m_impl;
 105     m_impl = 0;
 106 }
 107
 108 int IndexTool::Help(void) {
 109     Options::DisplayHelp();
 110     return 0;
 111 }
 112
 113 int IndexTool::Run(int argc, char* argv[]) {
 114
 115     // parse command line arguments
 116     Options::Parse(argc, argv, 1);
 117
 118     // initialize IndexTool with settings
 119     m_impl = new IndexToolPrivate(m_settings);
 120
 121     // run IndexTool, return success/fail
 122     if ( m_impl->Run() )
 123         return 0;
 124     else
 125         return 1;
 126 }