Reorganized source tree & build system

[bamtools.git] / src / toolkit / bamtools_header.cpp

diff --git a/src/toolkit/bamtools_header.cpp b/src/toolkit/bamtools_header.cpp
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+// ***************************************************************************
+// bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 1 June 2010
+// ---------------------------------------------------------------------------
+// Prints the SAM-style header from a single BAM file ( or merged header from
+// multiple BAM files) to stdout
+// ***************************************************************************
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "bamtools_header.h"
+#include "bamtools_options.h"
+#include "BamReader.h"
+#include "BamMultiReader.h"
+
+using namespace std;
+using namespace BamTools; 
+  
+// ---------------------------------------------
+// HeaderSettings implementation
+
+struct HeaderTool::HeaderSettings {
+
+    // flags
+    bool HasInputBamFilename;
+
+    // filenames
+    vector<string> InputFiles;
+    
+    // constructor
+    HeaderSettings(void)
+        : HasInputBamFilename(false)
+    { }
+};  
+
+// ---------------------------------------------
+// HeaderTool implementation
+
+HeaderTool::HeaderTool(void)
+    : AbstractTool()
+    , m_settings(new HeaderSettings)
+{
+    // set program details
+    Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "-in <filename> [-in <filename> ... ] ");
+    
+    // set up options 
+    OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+    Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+}
+
+HeaderTool::~HeaderTool(void) {
+    delete m_settings;
+    m_settings = 0;
+}
+
+int HeaderTool::Help(void) {
+    Options::DisplayHelp();
+    return 0;
+}
+
+int HeaderTool::Run(int argc, char* argv[]) {
+  
+    // parse command line arguments
+    Options::Parse(argc, argv, 1);
+  
+    // set to default input if none provided
+    if ( !m_settings->HasInputBamFilename ) 
+        m_settings->InputFiles.push_back(Options::StandardIn());
+    
+    // open files
+    BamMultiReader reader;
+    if ( reader.Open(m_settings->InputFiles, false) ) {      
+        // dump header contents to stdout
+        cout << reader.GetHeaderText() << endl;
+    }
+        
+    // clean up & exit
+    reader.Close();
+    return 0;
+}
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