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: 26 May 2010
7 // ---------------------------------------------------------------------------
8 // Creates a BAM index (".bai") file for the provided BAM file.
9 // ***************************************************************************
14 #include "bamtools_index.h"
15 #include "bamtools_options.h"
16 #include "BamReader.h"
19 using namespace BamTools;
21 // ---------------------------------------------
22 // IndexSettings implementation
24 struct IndexTool::IndexSettings {
27 bool HasInputBamFilename;
30 string InputBamFilename;
34 : HasInputBamFilename(false)
35 , InputBamFilename(Options::StandardIn())
39 // ---------------------------------------------
40 // IndexTool implementation
42 IndexTool::IndexTool(void)
44 , m_settings(new IndexSettings)
46 // set program details
47 Options::SetProgramInfo("bamtools index", "creates index for BAM file", "-in <filename>");
50 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
51 Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
54 IndexTool::~IndexTool(void) {
59 int IndexTool::Help(void) {
60 Options::DisplayHelp();
64 int IndexTool::Run(int argc, char* argv[]) {
66 // parse command line arguments
67 Options::Parse(argc, argv, 1);
69 // open our BAM reader
71 reader.Open(m_settings->InputBamFilename);
73 // create index for BAM file