// ***************************************************************************
// 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: 10 December 2012
// ---------------------------------------------------------------------------
// 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 <fstream>
#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;
+ bool HasInput;
+ bool HasInputFilelist;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
// constructor
HeaderSettings(void)
- : HasInputBamFilename(false)
+ : HasInput(false)
+ , HasInputFilelist(false)
{ }
};
+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->HasInput && !m_settings->HasInputFilelist )
+ m_settings->InputFiles.push_back(Options::StandardIn());
+
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools header ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
+ // 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> ... | -list <filelist>]");
// 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());
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
}
HeaderTool::~HeaderTool(void) {
+
delete m_settings;
m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
}
int HeaderTool::Help(void) {
// 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;
+}