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 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 7 April 2011
   7 // ---------------------------------------------------------------------------
   8 // Creates a BAM index file
   9 // ***************************************************************************
  10
  11 #include "bamtools_index.h"
  12
  13 #include <api/BamReader.h>
  14 #include <utils/bamtools_options.h>
  15 using namespace BamTools;
  16
  17 #include <iostream>
  18 #include <string>
  19 using namespace std;
  20
  21 // ---------------------------------------------
  22 // IndexSettings implementation
  23
  24 struct IndexTool::IndexSettings {
  25
  26     // flags
  27     bool HasInputBamFilename;
  28     bool IsUsingBamtoolsIndex;
  29
  30     // filenames
  31     string InputBamFilename;
  32
  33     // constructor
  34     IndexSettings(void)
  35         : HasInputBamFilename(false)
  36         , IsUsingBamtoolsIndex(false)
  37         , InputBamFilename(Options::StandardIn())
  38     { }
  39 };
  40
  41 // ---------------------------------------------
  42 // IndexToolPrivate implementation
  43
  44 struct IndexTool::IndexToolPrivate {
  45
  46     // ctor & dtor
  47     public:
  48         IndexToolPrivate(IndexTool::IndexSettings* settings)
  49             : m_settings(settings)
  50         { }
  51
  52         ~IndexToolPrivate(void) { }
  53
  54     // interface
  55     public:
  56         bool Run(void);
  57
  58     // data members
  59     private:
  60         IndexTool::IndexSettings* m_settings;
  61 };
  62
  63 bool IndexTool::IndexToolPrivate::Run(void) {
  64
  65     // open our BAM reader
  66     BamReader reader;
  67     if ( !reader.Open(m_settings->InputBamFilename) ) {
  68         cerr << "bamtools index ERROR: could not open BAM file: "
  69              << m_settings->InputBamFilename << endl;
  70         return false;
  71     }
  72
  73     // create index for BAM file
  74     const BamIndex::IndexType type = ( m_settings->IsUsingBamtoolsIndex ? BamIndex::BAMTOOLS
  75                                                                         : BamIndex::STANDARD );
  76     reader.CreateIndex(type);
  77
  78     // clean & exit
  79     reader.Close();
  80     return true;
  81 }
  82
  83 // ---------------------------------------------
  84 // IndexTool implementation
  85
  86 IndexTool::IndexTool(void)
  87     : AbstractTool()
  88     , m_settings(new IndexSettings)
  89     , m_impl(0)
  90 {
  91     // set program details
  92     Options::SetProgramInfo("bamtools index", "creates index for BAM file", "[-in <filename>] [-bti]");
  93
  94     // set up options
  95     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
  96     Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
  97     Options::AddOption("-bti", "create (non-standard) BamTools index file (*.bti). Default behavior is to create standard BAM index (*.bai)", m_settings->IsUsingBamtoolsIndex, IO_Opts);
  98 }
  99
 100 IndexTool::~IndexTool(void) {
 101
 102     delete m_settings;
 103     m_settings = 0;
 104
 105     delete m_impl;
 106     m_impl = 0;
 107 }
 108
 109 int IndexTool::Help(void) {
 110     Options::DisplayHelp();
 111     return 0;
 112 }
 113
 114 int IndexTool::Run(int argc, char* argv[]) {
 115
 116     // parse command line arguments
 117     Options::Parse(argc, argv, 1);
 118
 119     // initialize IndexTool with settings
 120     m_impl = new IndexToolPrivate(m_settings);
 121
 122     // run IndexTool, return success/fail
 123     if ( m_impl->Run() )
 124         return 0;
 125     else
 126         return 1;
 127 }