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: 7 April 2011
7 // ---------------------------------------------------------------------------
8 // Prints the SAM-style header from a single BAM file ( or merged header from
9 // multiple BAM files) to stdout
10 // ***************************************************************************
12 #include "bamtools_header.h"
14 #include <api/BamMultiReader.h>
15 #include <utils/bamtools_options.h>
16 using namespace BamTools;
23 // ---------------------------------------------
24 // HeaderSettings implementation
26 struct HeaderTool::HeaderSettings {
29 bool HasInputBamFilename;
32 vector<string> InputFiles;
36 : HasInputBamFilename(false)
40 struct HeaderTool::HeaderToolPrivate {
44 HeaderToolPrivate(HeaderTool::HeaderSettings* settings)
45 : m_settings(settings)
48 ~HeaderToolPrivate(void) { }
56 HeaderTool::HeaderSettings* m_settings;
59 bool HeaderTool::HeaderToolPrivate::Run(void) {
61 // set to default input if none provided
62 if ( !m_settings->HasInputBamFilename )
63 m_settings->InputFiles.push_back(Options::StandardIn());
65 // attemp to open BAM files
66 BamMultiReader reader;
67 if ( !reader.Open(m_settings->InputFiles) ) {
68 cerr << "bamtools header ERROR: could not open BAM file(s) for reading... Aborting." << endl;
72 // dump (merged) header contents to stdout
73 cout << reader.GetHeaderText() << endl;
80 // ---------------------------------------------
81 // HeaderTool implementation
83 HeaderTool::HeaderTool(void)
85 , m_settings(new HeaderSettings)
88 // set program details
89 Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "[-in <filename> -in <filename> ...] ");
92 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
93 Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
96 HeaderTool::~HeaderTool(void) {
105 int HeaderTool::Help(void) {
106 Options::DisplayHelp();
110 int HeaderTool::Run(int argc, char* argv[]) {
112 // parse command line arguments
113 Options::Parse(argc, argv, 1);
115 // initialize HeaderTool with settings
116 m_impl = new HeaderToolPrivate(m_settings);
118 // run HeaderTool, return success/fail