1 // ***************************************************************************
2 // bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 1 June 2010
7 // ---------------------------------------------------------------------------
8 // Prints the SAM-style header from a single BAM file ( or merged header from
9 // multiple BAM files) to stdout
10 // ***************************************************************************
16 #include "bamtools_header.h"
17 #include "bamtools_options.h"
18 #include "BamReader.h"
19 #include "BamMultiReader.h"
22 using namespace BamTools;
24 // ---------------------------------------------
25 // HeaderSettings implementation
27 struct HeaderTool::HeaderSettings {
30 bool HasInputBamFilename;
33 vector<string> InputFiles;
37 : HasInputBamFilename(false)
41 // ---------------------------------------------
42 // HeaderTool implementation
44 HeaderTool::HeaderTool(void)
46 , m_settings(new HeaderSettings)
48 // set program details
49 Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "-in <filename> [-in <filename> ... ] ");
52 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
53 Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
56 HeaderTool::~HeaderTool(void) {
61 int HeaderTool::Help(void) {
62 Options::DisplayHelp();
66 int HeaderTool::Run(int argc, char* argv[]) {
68 // parse command line arguments
69 Options::Parse(argc, argv, 1);
71 // set to default input if none provided
72 if ( !m_settings->HasInputBamFilename )
73 m_settings->InputFiles.push_back(Options::StandardIn());
76 BamMultiReader reader;
77 if ( reader.Open(m_settings->InputFiles, false) ) {
78 // dump header contents to stdout
79 cout << reader.GetHeaderText() << endl;