// ***************************************************************************
// bamtools_index.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 September 2010
+// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
-// Creates a BAM index (".bai") file for the provided BAM file.
+// Creates a BAM index file
// ***************************************************************************
-#include <iostream>
-#include <string>
-
#include "bamtools_index.h"
-#include "bamtools_options.h"
-#include "BamReader.h"
-using namespace std;
+#include <api/BamReader.h>
+#include <utils/bamtools_options.h>
using namespace BamTools;
+#include <iostream>
+#include <string>
+using namespace std;
+
// ---------------------------------------------
// IndexSettings implementation
{ }
};
+// ---------------------------------------------
+// IndexToolPrivate implementation
+
+struct IndexTool::IndexToolPrivate {
+
+ // ctor & dtor
+ public:
+ IndexToolPrivate(IndexTool::IndexSettings* settings)
+ : m_settings(settings)
+ { }
+
+ ~IndexToolPrivate(void) { }
+
+ // interface
+ public:
+ bool Run(void);
+
+ // data members
+ private:
+ IndexTool::IndexSettings* m_settings;
+};
+
+bool IndexTool::IndexToolPrivate::Run(void) {
+
+ // open our BAM reader
+ BamReader reader;
+ if ( !reader.Open(m_settings->InputBamFilename) ) {
+ cerr << "bamtools index ERROR: could not open BAM file: "
+ << m_settings->InputBamFilename << endl;
+ return false;
+ }
+
+ // create index for BAM file
+ const BamIndex::IndexType type = ( m_settings->IsUsingBamtoolsIndex ? BamIndex::BAMTOOLS
+ : BamIndex::STANDARD );
+ reader.CreateIndex(type);
+
+ // clean & exit
+ reader.Close();
+ return true;
+}
+
// ---------------------------------------------
// IndexTool implementation
IndexTool::IndexTool(void)
: AbstractTool()
, m_settings(new IndexSettings)
+ , m_impl(0)
{
// set program details
Options::SetProgramInfo("bamtools index", "creates index for BAM file", "[-in <filename>] [-bti]");
}
IndexTool::~IndexTool(void) {
+
delete m_settings;
m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
}
int IndexTool::Help(void) {
// parse command line arguments
Options::Parse(argc, argv, 1);
- // open our BAM reader
- BamReader reader;
- reader.Open(m_settings->InputBamFilename);
-
- // create index for BAM file
- bool useDefaultIndex = !m_settings->IsUsingBamtoolsIndex;
- reader.CreateIndex(useDefaultIndex);
-
- // clean & exit
- reader.Close();
- return 0;
+ // initialize IndexTool with settings
+ m_impl = new IndexToolPrivate(m_settings);
+
+ // run IndexTool, return success/fail
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
}