Fixed: improper mode check in local I/O device

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

diff --git a/src/toolkit/bamtools_header.cpp b/src/toolkit/bamtools_header.cpp
index b75f9a0e558b192cdac42350552881158efdc3c9..a08c632defa5bbbce75609f040e03d7a536c28da 100644 (file)
--- a/src/toolkit/bamtools_header.cpp
+++ b/src/toolkit/bamtools_header.cpp
@@ -1,25 +1,23 @@
 // ***************************************************************************
 // bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 7 April 2011
 // ---------------------------------------------------------------------------
 // Prints the SAM-style header from a single BAM file ( or merged header from
 // multiple BAM files) to stdout
 // ***************************************************************************
 
+#include "bamtools_header.h"
+
+#include <api/BamMultiReader.h>
+#include <utils/bamtools_options.h>
+using namespace BamTools;
+
 #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
@@ -38,15 +36,56 @@ struct HeaderTool::HeaderSettings {
     { }
 };  
 
+struct HeaderTool::HeaderToolPrivate {
+
+    // ctor & dtor
+    public:
+        HeaderToolPrivate(HeaderTool::HeaderSettings* settings)
+            : m_settings(settings)
+        { }
+
+        ~HeaderToolPrivate(void) { }
+
+    // interface
+    public:
+        bool Run(void);
+
+    // data members
+    private:
+        HeaderTool::HeaderSettings* m_settings;
+};
+
+bool HeaderTool::HeaderToolPrivate::Run(void) {
+
+    // set to default input if none provided
+    if ( !m_settings->HasInputBamFilename )
+        m_settings->InputFiles.push_back(Options::StandardIn());
+
+    // attemp to open BAM files
+    BamMultiReader reader;
+    if ( !reader.Open(m_settings->InputFiles) ) {
+        cerr << "bamtools header ERROR: could not open BAM file(s) for reading... Aborting." << endl;
+        return false;
+    }
+
+    // dump (merged) header contents to stdout
+    cout << reader.GetHeaderText() << endl;
+
+    // clean up & exit
+    reader.Close();
+    return true;
+}
+
 // ---------------------------------------------
 // HeaderTool implementation
 
 HeaderTool::HeaderTool(void)
     : AbstractTool()
     , m_settings(new HeaderSettings)
+    , m_impl(0)
 {
     // set program details
-    Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "-in <filename> [-in <filename> ... ] ");
+    Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "[-in <filename> -in <filename> ...] ");
     
     // set up options 
     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
@@ -54,8 +93,12 @@ HeaderTool::HeaderTool(void)
 }
 
 HeaderTool::~HeaderTool(void) {
+
     delete m_settings;
     m_settings = 0;
+
+    delete m_impl;
+    m_impl = 0;
 }
 
 int HeaderTool::Help(void) {
@@ -68,18 +111,12 @@ 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;
-}
\ No newline at end of file
+    // initialize HeaderTool with settings
+    m_impl = new HeaderToolPrivate(m_settings);
+
+    // run HeaderTool, return success/fail
+    if ( m_impl->Run() )
+        return 0;
+    else
+        return 1;
+}