(or the Windows equivalent)\n")
# set BamTools version information
-set (BamTools_VERSION_MAJOR 1)
+set (BamTools_VERSION_MAJOR 2)
set (BamTools_VERSION_MINOR 0)
-set (BamTools_VERSION_BUILD 2)
+set (BamTools_VERSION_BUILD 0)
# set our library and executable destination dirs
set (EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin")
#ifndef BAMALGORITHMS_H
#define BAMALGORITHMS_H
-#include <api/algorithms/Sort.h>
+#include "api/algorithms/Sort.h"
/*! \namespace BamTools::Algorithms
\brief Provides convenient classes & methods for working with BAM data
// Provides the BamAlignment data structure
// ***************************************************************************
-#include <api/BamAlignment.h>
-#include <api/BamConstants.h>
+#include "api/BamAlignment.h"
+#include "api/BamConstants.h"
using namespace BamTools;
using namespace std;
#ifndef BAMALIGNMENT_H
#define BAMALIGNMENT_H
-#include <api/api_global.h>
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
+#include "api/api_global.h"
+#include "api/BamAux.h"
+#include "api/BamConstants.h"
#include <cstdlib>
#include <cstring>
#include <string>
#ifndef BAMAUX_H\r
#define BAMAUX_H\r
\r
-#include <api/api_global.h>\r
+#include "api/api_global.h"\r
#include <fstream> \r
#include <iostream>\r
#include <string>\r
#ifndef BAM_CONSTANTS_H
#define BAM_CONSTANTS_H
-#include <api/api_global.h>
+#include "api/api_global.h"
#include <cassert>
#include <string>
// BamIndex.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 9 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic BAM index interface
// ***************************************************************************
#ifndef BAM_INDEX_H
#define BAM_INDEX_H
-#include <api/api_global.h>
-#include <api/BamAux.h>
+#include "api/api_global.h"
+#include "api/BamAux.h"
#include <string>
namespace BamTools {
// precludes the need to sort merged files.
// ***************************************************************************
-#include <api/BamMultiReader.h>
-#include <api/internal/BamMultiReader_p.h>
+#include "api/BamMultiReader.h"
+#include "api/internal/BamMultiReader_p.h"
using namespace BamTools;
#include <string>
// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Convenience class for reading multiple BAM files.
// ***************************************************************************
#ifndef BAMMULTIREADER_H
#define BAMMULTIREADER_H
-#include <api/api_global.h>
-#include <api/BamReader.h>
+#include "api/api_global.h"
+#include "api/BamReader.h"
#include <map>
#include <sstream>
#include <string>
// Provides read access to BAM files.
// ***************************************************************************
-#include <api/BamReader.h>
-#include <api/internal/BamReader_p.h>
+#include "api/BamReader.h"
+#include "api/internal/BamReader_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
// Marth Lab, Department of Biology, Boston College\r
// ---------------------------------------------------------------------------\r
-// Last modified: 7 October 2011 (DB)\r
+// Last modified: 10 October 2011 (DB)\r
// ---------------------------------------------------------------------------\r
// Provides read access to BAM files.\r
// ***************************************************************************\r
#ifndef BAMREADER_H\r
#define BAMREADER_H\r
\r
-#include <api/api_global.h>\r
-#include <api/BamAlignment.h>\r
-#include <api/BamIndex.h>\r
-#include <api/SamHeader.h>\r
+#include "api/api_global.h"\r
+#include "api/BamAlignment.h"\r
+#include "api/BamIndex.h"\r
+#include "api/SamHeader.h"\r
#include <string>\r
\r
namespace BamTools {\r
// Provides the basic functionality for producing BAM files\r
// ***************************************************************************\r
\r
-#include <api/BamAlignment.h>\r
-#include <api/BamWriter.h>\r
-#include <api/SamHeader.h>\r
-#include <api/internal/BamWriter_p.h>\r
+#include "api/BamAlignment.h"\r
+#include "api/BamWriter.h"\r
+#include "api/SamHeader.h"\r
+#include "api/internal/BamWriter_p.h"\r
using namespace BamTools;\r
using namespace BamTools::Internal;\r
using namespace std;\r
#ifndef BAMWRITER_H\r
#define BAMWRITER_H\r
\r
-#include <api/api_global.h>\r
-#include <api/BamAux.h>\r
+#include "api/api_global.h"\r
+#include "api/BamAux.h"\r
#include <string>\r
\r
namespace BamTools {\r
# create main BamTools API shared library
add_library( BamTools SHARED ${BamToolsAPISources} )
-set_target_properties( BamTools PROPERTIES SOVERSION "1.0.2" )
+set_target_properties( BamTools PROPERTIES SOVERSION "2.0.0" )
set_target_properties( BamTools PROPERTIES OUTPUT_NAME "bamtools" )
# create main BamTools API static library
// IBamIODevice.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Base class for all BAM I/O devices (e.g. local file, pipe, HTTP, FTP, etc.)
//
#ifndef IBAMIODEVICE_H
#define IBAMIODEVICE_H
-#include <api/api_global.h>
+#include "api/api_global.h"
#include <string>
namespace BamTools {
// SamConstants.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides constants for SAM header
// ***************************************************************************
#ifndef SAM_CONSTANTS_H
#define SAM_CONSTANTS_H
-#include <api/api_global.h>
+#include "api/api_global.h"
#include <string>
namespace BamTools {
// Provides direct read/write access to the SAM header data fields.
// ***************************************************************************
-#include <api/SamConstants.h>
-#include <api/SamHeader.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/SamFormatParser_p.h>
-#include <api/internal/SamFormatPrinter_p.h>
-#include <api/internal/SamHeaderValidator_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/SamFormatParser_p.h"
+#include "api/internal/SamFormatPrinter_p.h"
+#include "api/internal/SamHeaderValidator_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
using namespace std;
#ifndef SAM_HEADER_H
#define SAM_HEADER_H
-#include <api/api_global.h>
-#include <api/SamProgramChain.h>
-#include <api/SamReadGroupDictionary.h>
-#include <api/SamSequenceDictionary.h>
+#include "api/api_global.h"
+#include "api/SamProgramChain.h"
+#include "api/SamReadGroupDictionary.h"
+#include "api/SamSequenceDictionary.h"
#include <string>
#include <vector>
// SamProgram.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides direct read/write access to the SAM header program records.
// ***************************************************************************
-#include <api/SamProgram.h>
+#include "api/SamProgram.h"
using namespace BamTools;
using namespace std;
// Provides methods for operating on a SamProgram record "chain"
// ***************************************************************************
-#include <api/SamProgramChain.h>
+#include "api/SamProgramChain.h"
using namespace BamTools;
#include <algorithm>
#ifndef SAM_PROGRAMCHAIN_H
#define SAM_PROGRAMCHAIN_H
-#include <api/api_global.h>
-#include <api/SamProgram.h>
+#include "api/api_global.h"
+#include "api/SamProgram.h"
#include <string>
#include <vector>
// SamReadGroup.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides direct read/write access to the SAM read group data fields.
// ***************************************************************************
-#include <api/SamReadGroup.h>
+#include "api/SamReadGroup.h"
using namespace BamTools;
using namespace std;
// Provides methods for operating on a collection of SamReadGroup entries.
// ***************************************************************************
-#include <api/SamReadGroupDictionary.h>
+#include "api/SamReadGroupDictionary.h"
using namespace BamTools;
#include <algorithm>
// SamReadGroupDictionary.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 1 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamReadGroup entries.
// ***************************************************************************
#ifndef SAM_READGROUP_DICTIONARY_H
#define SAM_READGROUP_DICTIONARY_H
-#include <api/api_global.h>
-#include <api/SamReadGroup.h>
+#include "api/api_global.h"
+#include "api/SamReadGroup.h"
#include <string>
#include <vector>
// SamSequence.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides direct read/write access to the SAM sequence data fields.
// ***************************************************************************
-#include <api/SamSequence.h>
+#include "api/SamSequence.h"
#include <sstream>
using namespace BamTools;
using namespace std;
#ifndef SAM_SEQUENCE_H
#define SAM_SEQUENCE_H
-#include <api/api_global.h>
+#include "api/api_global.h"
#include <string>
namespace BamTools {
#ifndef ALGORITHMS_SORT_H
#define ALGORITHMS_SORT_H
-#include <api/api_global.h>
-#include <api/BamAlignment.h>
-#include <api/BamReader.h>
-#include <api/BamMultiReader.h>
+#include "api/api_global.h"
+#include "api/BamAlignment.h"
+#include "api/BamReader.h"
+#include "api/BamMultiReader.h"
#include <cassert>
#include <algorithm>
#include <functional>
// BamDeviceFactory_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 September 2011 (DB)
// ---------------------------------------------------------------------------
// Creates built-in concrete implementations of IBamIODevices
// ***************************************************************************
-#include <api/internal/BamDeviceFactory_p.h>
-#include <api/internal/BamFile_p.h>
-#include <api/internal/BamFtp_p.h>
-#include <api/internal/BamHttp_p.h>
-#include <api/internal/BamPipe_p.h>
+#include "api/internal/BamDeviceFactory_p.h"
+#include "api/internal/BamFile_p.h"
+#include "api/internal/BamFtp_p.h"
+#include "api/internal/BamHttp_p.h"
+#include "api/internal/BamPipe_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamDeviceFactory_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Creates built-in concrete implementations of IBamIODevices
// ***************************************************************************
//
// We mean it.
-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"
#include <string>
namespace BamTools {
// BamException_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 5 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides a basic exception class for BamTools internals
// ***************************************************************************
-#include <api/internal/BamException_p.h>
+#include "api/internal/BamException_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
using namespace std;
// BamFile_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides BAM file-specific IO behavior
// ***************************************************************************
-#include <api/internal/BamFile_p.h>
+#include "api/internal/BamFile_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamFile_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 9 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides BAM file-specific IO behavior
// ***************************************************************************
//
// We mean it.
-#include <api/internal/ILocalIODevice_p.h>
+#include "api/internal/ILocalIODevice_p.h"
#include <string>
namespace BamTools {
// BamFtp_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 9 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides reading/writing of BAM files on FTP server
// ***************************************************************************
-#include <api/internal/BamFtp_p.h>
+#include "api/internal/BamFtp_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamFtp_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides reading/writing of BAM files on FTP server
// ***************************************************************************
//
// We mean it.
-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"
#include <string>
namespace BamTools {
// BamHeader_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for handling BAM headers.
// ***************************************************************************
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamHeader_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAux.h"
+#include "api/BamConstants.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BgzfStream_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamHeader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for handling BAM headers.
// ***************************************************************************
//
// We mean it.
-#include <api/SamHeader.h>
+#include "api/SamHeader.h"
#include <string>
namespace BamTools {
// BamHttp_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 9 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides reading/writing of BAM files on HTTP server
// ***************************************************************************
-#include <api/internal/BamHttp_p.h>
+#include "api/internal/BamHttp_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamHttp_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides reading/writing of BAM files on HTTP server
// ***************************************************************************
//
// We mean it.
-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"
#include <string>
namespace BamTools {
// BamIndexFactory_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides interface for generating BamIndex implementations
// ***************************************************************************
-#include <api/BamAux.h>
-#include <api/internal/BamIndexFactory_p.h>
-#include <api/internal/BamStandardIndex_p.h>
-#include <api/internal/BamToolsIndex_p.h>
+#include "api/BamAux.h"
+#include "api/internal/BamIndexFactory_p.h"
+#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/BamToolsIndex_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
using namespace std;
// BamIndexFactory_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides interface for generating BamIndex implementations
// ***************************************************************************
#ifndef BAMINDEX_FACTORY_P_H
#define BAMINDEX_FACTORY_P_H
-#include <api/BamIndex.h>
+#include "api/BamIndex.h"
#include <string>
namespace BamTools {
// BamMultiMerger_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 3 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides merging functionality for BamMultiReader. At this point, supports
// sorting results by (refId, position) or by read name.
//
// We mean it.
-#include <api/BamAlignment.h>
-#include <api/BamReader.h>
-#include <api/algorithms/Sort.h>
+#include "api/BamAlignment.h"
+#include "api/BamReader.h"
+#include "api/algorithms/Sort.h"
#include <deque>
#include <functional>
#include <set>
// BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// *************************************************************************
-#include <api/BamAlignment.h>
-#include <api/BamMultiReader.h>
-#include <api/SamConstants.h>
-#include <api/algorithms/Sort.h>
-#include <api/internal/BamMultiReader_p.h>
+#include "api/BamAlignment.h"
+#include "api/BamMultiReader.h"
+#include "api/SamConstants.h"
+#include "api/algorithms/Sort.h"
+#include "api/internal/BamMultiReader_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamMultiReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// *************************************************************************
//
// We mean it.
-#include <api/SamHeader.h>
-#include <api/BamMultiReader.h>
-#include <api/internal/BamMultiMerger_p.h>
+#include "api/SamHeader.h"
+#include "api/BamMultiReader.h"
+#include "api/internal/BamMultiMerger_p.h"
#include <string>
#include <vector>
// BamPipe_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides BAM pipe-specific IO behavior
// ***************************************************************************
-#include <api/internal/BamPipe_p.h>
+#include "api/internal/BamPipe_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamPipe_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides BAM pipe-specific IO behavior
// ***************************************************************************
//
// We mean it.
-#include <api/internal/ILocalIODevice_p.h>
+#include "api/internal/ILocalIODevice_p.h"
#include <string>
namespace BamTools {
// BamRandomAccessController_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011(DB)
+// Last modified: 10 October 2011(DB)
// ---------------------------------------------------------------------------
// Manages random access operations in a BAM file
// **************************************************************************
-#include <api/BamIndex.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamIndexFactory_p.h>
+#include "api/BamIndex.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamIndexFactory_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamRandomAccessController_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011(DB)
+// Last modified: 10 October 2011(DB)
// ---------------------------------------------------------------------------
// Manages random access operations in a BAM file
// ***************************************************************************
//
// We mean it.
-#include <api/BamAux.h>
-#include <api/BamIndex.h>
+#include "api/BamAux.h"
+#include "api/BamIndex.h"
namespace BamTools {
// BamReader_p.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for reading BAM files
// ***************************************************************************
-#include <api/BamConstants.h>
-#include <api/BamReader.h>
-#include <api/IBamIODevice.h>
-#include <api/internal/BamDeviceFactory_p.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamHeader_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamStandardIndex_p.h>
-#include <api/internal/BamToolsIndex_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamConstants.h"
+#include "api/BamReader.h"
+#include "api/IBamIODevice.h"
+#include "api/internal/BamDeviceFactory_p.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/BamToolsIndex_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for reading BAM files
// ***************************************************************************
//
// We mean it.
-#include <api/BamAlignment.h>
-#include <api/BamIndex.h>
-#include <api/BamReader.h>
-#include <api/SamHeader.h>
-#include <api/internal/BamHeader_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAlignment.h"
+#include "api/BamIndex.h"
+#include "api/BamReader.h"
+#include "api/SamHeader.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BgzfStream_p.h"
#include <string>
namespace BamTools {
// BamStandardIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the standardized BAM index format (".bai")
// ***************************************************************************
-#include <api/BamAlignment.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamStandardIndex_p.h>
+#include "api/BamAlignment.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamStandardIndex_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamStandardIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the standardized BAM index format (".bai")
// ***************************************************************************
//
// We mean it.
-#include <api/BamAux.h>
-#include <api/BamIndex.h>
+#include "api/BamAux.h"
+#include "api/BamIndex.h"
#include <map>
#include <set>
#include <string>
// BamToolsIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the BamTools index format (".bti")
// ***************************************************************************
-#include <api/BamAlignment.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamToolsIndex_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAlignment.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamToolsIndex_p.h"
+#include "api/internal/BgzfStream_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// BamToolsIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the BamTools index format (".bti")
// ***************************************************************************
//
// We mean it.
-#include <api/BamAux.h>
-#include <api/BamIndex.h>
+#include "api/BamAux.h"
+#include "api/BamIndex.h"
#include <map>
#include <string>
#include <vector>
// BamWriter_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for producing BAM files
// ***************************************************************************
-#include <api/BamAlignment.h>
-#include <api/BamConstants.h>
-#include <api/IBamIODevice.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamWriter_p.h>
+#include "api/BamAlignment.h"
+#include "api/BamConstants.h"
+#include "api/IBamIODevice.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamWriter_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
try {
// open the BGZF file for writing
- m_stream.Open(filename, IBamIODevice::WriteOnly);
+ m_stream.Open(filename, IBamIODevice::WriteOnly);
// write BAM file 'metadata' components
WriteMagicNumber();
// BamWriter_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for producing BAM files
// ***************************************************************************
//
// We mean it.
-#include <api/BamAux.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAux.h"
+#include "api/internal/BgzfStream_p.h"
#include <string>
#include <vector>
// BgzfStream_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011(DB)
+// Last modified: 10 October 2011(DB)
// ---------------------------------------------------------------------------
// Based on BGZF routines developed at the Broad Institute.
// Provides the basic functionality for reading & writing BGZF files
// Replaces the old BGZF.* files to avoid clashing with other toolkits
// ***************************************************************************
-#include <api/internal/BamDeviceFactory_p.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAux.h"
+#include "api/BamConstants.h"
+#include "api/internal/BamDeviceFactory_p.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BgzfStream_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
+#include "zlib.h"
+
#include <cstring>
#include <algorithm>
#include <iostream>
// BgzfStream_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011(DB)
+// Last modified: 10 October 2011(DB)
// ---------------------------------------------------------------------------
// Based on BGZF routines developed at the Broad Institute.
// Provides the basic functionality for reading & writing BGZF files
//
// We mean it.
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
-#include <api/IBamIODevice.h>
-#include "zlib.h"
-#include <cstdio>
-#include <memory>
+#include "api/api_global.h"
+#include "api/IBamIODevice.h"
#include <string>
namespace BamTools {
// ILocalIODevice_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides shared behavior for files & pipes
// ***************************************************************************
-#include <api/internal/ILocalIODevice_p.h>
+#include "api/internal/ILocalIODevice_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// ILocalIODevice_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides shared behavior for files & pipes
// ***************************************************************************
//
// We mean it.
-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"
namespace BamTools {
namespace Internal {
// SamFormatParser.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides functionality for parsing SAM header text into SamHeader object
// ***************************************************************************
-#include <api/SamConstants.h>
-#include <api/SamHeader.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/SamFormatParser_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/SamFormatParser_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// SamFormatPrinter.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides functionality for printing formatted SAM header to string
// ***************************************************************************
-#include <api/SamConstants.h>
-#include <api/SamHeader.h>
-#include <api/internal/SamFormatPrinter_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/SamFormatPrinter_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// SamHeaderValidator.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides functionality for validating SamHeader data
// ***************************************************************************
-#include <api/SamConstants.h>
-#include <api/SamHeader.h>
-#include <api/internal/SamHeaderValidator_p.h>
-#include <api/internal/SamHeaderVersion_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/SamHeaderValidator_p.h"
+#include "api/internal/SamHeaderVersion_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// SamHeaderVersion.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 24 February 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides functionality for comparing SAM header versions
// *************************************************************************
//
// We mean it.
-#include <api/SamConstants.h>
+#include "api/SamConstants.h"
#include <sstream>
#include <string>
# set BamTools application properties
set_target_properties( bamtools_cmd PROPERTIES
- VERSION 1.0.2
+ VERSION 2.0.0
OUTPUT_NAME "bamtools"
)
# make version info available in application
# set BamTools library properties
set_target_properties( BamTools-utils PROPERTIES
- SOVERSION 1.0.2
+ SOVERSION 2.0.0
OUTPUT_NAME bamtools-utils
)
// bamtools_fasta.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 13 July 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides FASTA reading/indexing functionality.
// ***************************************************************************
-#include <utils/bamtools_fasta.h>
+#include "utils/bamtools_fasta.h"
using namespace BamTools;
#include <cstdio>
// bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides FASTA reading/indexing functionality.
// ***************************************************************************
#ifndef BAMTOOLS_FASTA_H
#define BAMTOOLS_FASTA_H
-#include <utils/utils_global.h>
+#include "utils/utils_global.h"
#include <string>
namespace BamTools {
// bamtools_filter_engine.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides a generic filter engine based on filter-sets of properties,
// with possible "rules" (compound logical expressions) to create more complex
#ifndef BAMTOOLS_FILTER_ENGINE_H
#define BAMTOOLS_FILTER_ENGINE_H
-#include <utils/bamtools_filter_properties.h>
-#include <utils/bamtools_filter_ruleparser.h>
-#include <utils/bamtools_utilities.h>
-#include <utils/utils_global.h>
+#include "utils/utils_global.h"
+#include "utils/bamtools_filter_properties.h"
+#include "utils/bamtools_filter_ruleparser.h"
+#include "utils/bamtools_utilities.h"
+
#include <algorithm>
#include <iostream>
#include <map>
// bamtools_filter_properties.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides support data structures & methods for FilterEngine
//
#ifndef BAMTOOLS_FILTER_PROPERTIES_H
#define BAMTOOLS_FILTER_PROPERTIES_H
-#include <utils/bamtools_utilities.h>
-#include <utils/bamtools_variant.h>
-#include <utils/utils_global.h>
+#include "utils/utils_global.h"
+#include "utils/bamtools_utilities.h"
+#include "utils/bamtools_variant.h"
#include <iostream>
#include <map>
#include <string>
// bamtools_filter_ruleparser.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides a compound rule parser for FilterEngine.
// ***************************************************************************
#ifndef BAMTOOLS_FILTER_RULEPARSER_H
#define BAMTOOLS_FILTER_RULEPARSER_H
-#include <utils/bamtools_utilities.h>
+#include "utils/bamtools_utilities.h"
#include <queue>
#include <stack>
#include <string>
// bamtools_options.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 11 June 2011
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Parses command line arguments and creates a help menu
// ---------------------------------------------------------------------------
// * (BamTools namespace, added stdin/stdout) (DB)
// ***************************************************************************
-#include <utils/bamtools_options.h>
+#include "utils/bamtools_options.h"
using namespace BamTools;
#include <cstdio>
// bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 11 June 2011
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Parses command line arguments and creates a help menu
// ---------------------------------------------------------------------------
#ifndef BAMTOOLS_OPTIONS_H
#define BAMTOOLS_OPTIONS_H
-#include <utils/bamtools_variant.h>
-#include <utils/utils_global.h>
+#include "utils/bamtools_variant.h"
+#include "utils/utils_global.h"
#include <map>
#include <string>
// bamtools_pileup_engine.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides pileup at position functionality for various tools.
// ***************************************************************************
-#include <utils/bamtools_pileup_engine.h>
+#include "utils/bamtools_pileup_engine.h"
using namespace BamTools;
#include <iostream>
// bamtools_pileup_engine.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 18 September 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides pileup at position functionality for various tools.
// ***************************************************************************
#ifndef BAMTOOLS_PILEUP_ENGINE_H
#define BAMTOOLS_PILEUP_ENGINE_H
+#include "utils/utils_global.h"
+
#include <api/BamAlignment.h>
-#include <utils/utils_global.h>
#include <vector>
namespace BamTools {
// bamtools_variant.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010
+// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides a template-based variant type
// ---------------------------------------------------------------------------
#ifndef BAMTOOLS_VARIANT_H
#define BAMTOOLS_VARIANT_H
-#include <utils/utils_global.h>
+#include "utils/utils_global.h"
#include <stdexcept>
#include <string>
#include <typeinfo>