From: derek Date: Mon, 10 Oct 2011 22:29:53 +0000 (-0400) Subject: Cleaned up intra-API includes & moved version numbers to 2.0.0 X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=commitdiff_plain;h=9f1ce8c47aeadb6dc1320b52ee671c3341b97935 Cleaned up intra-API includes & moved version numbers to 2.0.0 --- diff --git a/CMakeLists.txt b/CMakeLists.txt index 88beb4e..a04cf38 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -30,9 +30,9 @@ ensure_out_of_source_build (" (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") diff --git a/src/api/BamAlgorithms.h b/src/api/BamAlgorithms.h index 9493c7f..6109412 100644 --- a/src/api/BamAlgorithms.h +++ b/src/api/BamAlgorithms.h @@ -12,7 +12,7 @@ #ifndef BAMALGORITHMS_H #define BAMALGORITHMS_H -#include +#include "api/algorithms/Sort.h" /*! \namespace BamTools::Algorithms \brief Provides convenient classes & methods for working with BAM data diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp index d97c09f..78d7d6b 100644 --- a/src/api/BamAlignment.cpp +++ b/src/api/BamAlignment.cpp @@ -7,8 +7,8 @@ // Provides the BamAlignment data structure // *************************************************************************** -#include -#include +#include "api/BamAlignment.h" +#include "api/BamConstants.h" using namespace BamTools; using namespace std; diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h index daea418..9a8e7be 100644 --- a/src/api/BamAlignment.h +++ b/src/api/BamAlignment.h @@ -10,9 +10,9 @@ #ifndef BAMALIGNMENT_H #define BAMALIGNMENT_H -#include -#include -#include +#include "api/api_global.h" +#include "api/BamAux.h" +#include "api/BamConstants.h" #include #include #include diff --git a/src/api/BamAux.h b/src/api/BamAux.h index 29a0209..f451125 100644 --- a/src/api/BamAux.h +++ b/src/api/BamAux.h @@ -10,7 +10,7 @@ #ifndef BAMAUX_H #define BAMAUX_H -#include +#include "api/api_global.h" #include #include #include diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h index 7c115f1..a944096 100644 --- a/src/api/BamConstants.h +++ b/src/api/BamConstants.h @@ -10,7 +10,7 @@ #ifndef BAM_CONSTANTS_H #define BAM_CONSTANTS_H -#include +#include "api/api_global.h" #include #include diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h index e967c09..5e40d87 100644 --- a/src/api/BamIndex.h +++ b/src/api/BamIndex.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -10,8 +10,8 @@ #ifndef BAM_INDEX_H #define BAM_INDEX_H -#include -#include +#include "api/api_global.h" +#include "api/BamAux.h" #include namespace BamTools { diff --git a/src/api/BamMultiReader.cpp b/src/api/BamMultiReader.cpp index 8712aad..6efeff6 100644 --- a/src/api/BamMultiReader.cpp +++ b/src/api/BamMultiReader.cpp @@ -12,8 +12,8 @@ // precludes the need to sort merged files. // *************************************************************************** -#include -#include +#include "api/BamMultiReader.h" +#include "api/internal/BamMultiReader_p.h" using namespace BamTools; #include diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h index 1b1c270..76d0810 100644 --- a/src/api/BamMultiReader.h +++ b/src/api/BamMultiReader.h @@ -2,7 +2,7 @@ // 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. // *************************************************************************** @@ -10,8 +10,8 @@ #ifndef BAMMULTIREADER_H #define BAMMULTIREADER_H -#include -#include +#include "api/api_global.h" +#include "api/BamReader.h" #include #include #include diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp index 58a2f3f..6e4a10f 100644 --- a/src/api/BamReader.cpp +++ b/src/api/BamReader.cpp @@ -7,8 +7,8 @@ // Provides read access to BAM files. // *************************************************************************** -#include -#include +#include "api/BamReader.h" +#include "api/internal/BamReader_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamReader.h b/src/api/BamReader.h index 8e15a5c..30c4d5f 100644 --- a/src/api/BamReader.h +++ b/src/api/BamReader.h @@ -2,7 +2,7 @@ // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 7 October 2011 (DB) +// Last modified: 10 October 2011 (DB) // --------------------------------------------------------------------------- // Provides read access to BAM files. // *************************************************************************** @@ -10,10 +10,10 @@ #ifndef BAMREADER_H #define BAMREADER_H -#include -#include -#include -#include +#include "api/api_global.h" +#include "api/BamAlignment.h" +#include "api/BamIndex.h" +#include "api/SamHeader.h" #include namespace BamTools { diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp index 4120ccb..b1582a8 100644 --- a/src/api/BamWriter.cpp +++ b/src/api/BamWriter.cpp @@ -7,10 +7,10 @@ // Provides the basic functionality for producing BAM files // *************************************************************************** -#include -#include -#include -#include +#include "api/BamAlignment.h" +#include "api/BamWriter.h" +#include "api/SamHeader.h" +#include "api/internal/BamWriter_p.h" using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h index 6767a1c..68257ee 100644 --- a/src/api/BamWriter.h +++ b/src/api/BamWriter.h @@ -10,8 +10,8 @@ #ifndef BAMWRITER_H #define BAMWRITER_H -#include -#include +#include "api/api_global.h" +#include "api/BamAux.h" #include namespace BamTools { diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt index 2ec006c..c85b71b 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@ -49,7 +49,7 @@ set( BamToolsAPISources # 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 diff --git a/src/api/IBamIODevice.h b/src/api/IBamIODevice.h index 5c1856e..b34e449 100644 --- a/src/api/IBamIODevice.h +++ b/src/api/IBamIODevice.h @@ -2,7 +2,7 @@ // 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.) // @@ -18,7 +18,7 @@ #ifndef IBAMIODEVICE_H #define IBAMIODEVICE_H -#include +#include "api/api_global.h" #include namespace BamTools { diff --git a/src/api/SamConstants.h b/src/api/SamConstants.h index 913c213..405668c 100644 --- a/src/api/SamConstants.h +++ b/src/api/SamConstants.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -10,7 +10,7 @@ #ifndef SAM_CONSTANTS_H #define SAM_CONSTANTS_H -#include +#include "api/api_global.h" #include namespace BamTools { diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp index c2ec073..5de2abc 100644 --- a/src/api/SamHeader.cpp +++ b/src/api/SamHeader.cpp @@ -7,12 +7,12 @@ // Provides direct read/write access to the SAM header data fields. // *************************************************************************** -#include -#include -#include -#include -#include -#include +#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; diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h index b5f37a6..5004994 100644 --- a/src/api/SamHeader.h +++ b/src/api/SamHeader.h @@ -10,10 +10,10 @@ #ifndef SAM_HEADER_H #define SAM_HEADER_H -#include -#include -#include -#include +#include "api/api_global.h" +#include "api/SamProgramChain.h" +#include "api/SamReadGroupDictionary.h" +#include "api/SamSequenceDictionary.h" #include #include diff --git a/src/api/SamProgram.cpp b/src/api/SamProgram.cpp index fed9b8b..1720678 100644 --- a/src/api/SamProgram.cpp +++ b/src/api/SamProgram.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/SamProgram.h" using namespace BamTools; using namespace std; diff --git a/src/api/SamProgramChain.cpp b/src/api/SamProgramChain.cpp index 8213402..88c2185 100644 --- a/src/api/SamProgramChain.cpp +++ b/src/api/SamProgramChain.cpp @@ -7,7 +7,7 @@ // Provides methods for operating on a SamProgram record "chain" // *************************************************************************** -#include +#include "api/SamProgramChain.h" using namespace BamTools; #include diff --git a/src/api/SamProgramChain.h b/src/api/SamProgramChain.h index 7e24e5e..a2bd532 100644 --- a/src/api/SamProgramChain.h +++ b/src/api/SamProgramChain.h @@ -10,8 +10,8 @@ #ifndef SAM_PROGRAMCHAIN_H #define SAM_PROGRAMCHAIN_H -#include -#include +#include "api/api_global.h" +#include "api/SamProgram.h" #include #include diff --git a/src/api/SamReadGroup.cpp b/src/api/SamReadGroup.cpp index a9170d7..ce022ab 100644 --- a/src/api/SamReadGroup.cpp +++ b/src/api/SamReadGroup.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/SamReadGroup.h" using namespace BamTools; using namespace std; diff --git a/src/api/SamReadGroupDictionary.cpp b/src/api/SamReadGroupDictionary.cpp index 724f302..c501773 100644 --- a/src/api/SamReadGroupDictionary.cpp +++ b/src/api/SamReadGroupDictionary.cpp @@ -7,7 +7,7 @@ // Provides methods for operating on a collection of SamReadGroup entries. // *************************************************************************** -#include +#include "api/SamReadGroupDictionary.h" using namespace BamTools; #include diff --git a/src/api/SamReadGroupDictionary.h b/src/api/SamReadGroupDictionary.h index 89f23e0..7a651e1 100644 --- a/src/api/SamReadGroupDictionary.h +++ b/src/api/SamReadGroupDictionary.h @@ -2,7 +2,7 @@ // 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. // *************************************************************************** @@ -10,8 +10,8 @@ #ifndef SAM_READGROUP_DICTIONARY_H #define SAM_READGROUP_DICTIONARY_H -#include -#include +#include "api/api_global.h" +#include "api/SamReadGroup.h" #include #include diff --git a/src/api/SamSequence.cpp b/src/api/SamSequence.cpp index c8e375f..dea176b 100644 --- a/src/api/SamSequence.cpp +++ b/src/api/SamSequence.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/SamSequence.h" #include using namespace BamTools; using namespace std; diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h index aea59cc..c1a8792 100644 --- a/src/api/SamSequence.h +++ b/src/api/SamSequence.h @@ -10,7 +10,7 @@ #ifndef SAM_SEQUENCE_H #define SAM_SEQUENCE_H -#include +#include "api/api_global.h" #include namespace BamTools { diff --git a/src/api/algorithms/Sort.h b/src/api/algorithms/Sort.h index cf21479..92cb165 100644 --- a/src/api/algorithms/Sort.h +++ b/src/api/algorithms/Sort.h @@ -11,10 +11,10 @@ #ifndef ALGORITHMS_SORT_H #define ALGORITHMS_SORT_H -#include -#include -#include -#include +#include "api/api_global.h" +#include "api/BamAlignment.h" +#include "api/BamReader.h" +#include "api/BamMultiReader.h" #include #include #include diff --git a/src/api/internal/BamDeviceFactory_p.cpp b/src/api/internal/BamDeviceFactory_p.cpp index da0daad..895d08c 100644 --- a/src/api/internal/BamDeviceFactory_p.cpp +++ b/src/api/internal/BamDeviceFactory_p.cpp @@ -2,16 +2,16 @@ // 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 -#include -#include -#include -#include +#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; diff --git a/src/api/internal/BamDeviceFactory_p.h b/src/api/internal/BamDeviceFactory_p.h index f126831..1d48533 100644 --- a/src/api/internal/BamDeviceFactory_p.h +++ b/src/api/internal/BamDeviceFactory_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/IBamIODevice.h" #include namespace BamTools { diff --git a/src/api/internal/BamException_p.cpp b/src/api/internal/BamException_p.cpp index 38241d8..38469e7 100644 --- a/src/api/internal/BamException_p.cpp +++ b/src/api/internal/BamException_p.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/internal/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/internal/BamFile_p.cpp b/src/api/internal/BamFile_p.cpp index 3927d30..74c4ed6 100644 --- a/src/api/internal/BamFile_p.cpp +++ b/src/api/internal/BamFile_p.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/internal/BamFile_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamFile_p.h b/src/api/internal/BamFile_p.h index fd25a3e..873e71a 100644 --- a/src/api/internal/BamFile_p.h +++ b/src/api/internal/BamFile_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/internal/ILocalIODevice_p.h" #include namespace BamTools { diff --git a/src/api/internal/BamFtp_p.cpp b/src/api/internal/BamFtp_p.cpp index f957197..779d099 100644 --- a/src/api/internal/BamFtp_p.cpp +++ b/src/api/internal/BamFtp_p.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/internal/BamFtp_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamFtp_p.h b/src/api/internal/BamFtp_p.h index d410201..1f5ee0f 100644 --- a/src/api/internal/BamFtp_p.h +++ b/src/api/internal/BamFtp_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/IBamIODevice.h" #include namespace BamTools { diff --git a/src/api/internal/BamHeader_p.cpp b/src/api/internal/BamHeader_p.cpp index 7ec1181..dc734bf 100644 --- a/src/api/internal/BamHeader_p.cpp +++ b/src/api/internal/BamHeader_p.cpp @@ -2,16 +2,16 @@ // 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 -#include -#include -#include -#include +#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; diff --git a/src/api/internal/BamHeader_p.h b/src/api/internal/BamHeader_p.h index 42af68c..499ad96 100644 --- a/src/api/internal/BamHeader_p.h +++ b/src/api/internal/BamHeader_p.h @@ -2,7 +2,7 @@ // 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. // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/SamHeader.h" #include namespace BamTools { diff --git a/src/api/internal/BamHttp_p.cpp b/src/api/internal/BamHttp_p.cpp index 532194b..83b4c3b 100644 --- a/src/api/internal/BamHttp_p.cpp +++ b/src/api/internal/BamHttp_p.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/internal/BamHttp_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamHttp_p.h b/src/api/internal/BamHttp_p.h index e1d2403..38e94b7 100644 --- a/src/api/internal/BamHttp_p.h +++ b/src/api/internal/BamHttp_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/IBamIODevice.h" #include namespace BamTools { diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/BamIndexFactory_p.cpp index 4e9d1f2..2cf871f 100644 --- a/src/api/internal/BamIndexFactory_p.cpp +++ b/src/api/internal/BamIndexFactory_p.cpp @@ -2,15 +2,15 @@ // 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 -#include -#include -#include +#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; diff --git a/src/api/internal/BamIndexFactory_p.h b/src/api/internal/BamIndexFactory_p.h index 7b1ff96..4e4f1cf 100644 --- a/src/api/internal/BamIndexFactory_p.h +++ b/src/api/internal/BamIndexFactory_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -10,7 +10,7 @@ #ifndef BAMINDEX_FACTORY_P_H #define BAMINDEX_FACTORY_P_H -#include +#include "api/BamIndex.h" #include namespace BamTools { diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/BamMultiMerger_p.h index 2b7b110..3000097 100644 --- a/src/api/internal/BamMultiMerger_p.h +++ b/src/api/internal/BamMultiMerger_p.h @@ -2,7 +2,7 @@ // 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. @@ -21,9 +21,9 @@ // // We mean it. -#include -#include -#include +#include "api/BamAlignment.h" +#include "api/BamReader.h" +#include "api/algorithms/Sort.h" #include #include #include diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/BamMultiReader_p.cpp index f92258d..076f1bb 100644 --- a/src/api/internal/BamMultiReader_p.cpp +++ b/src/api/internal/BamMultiReader_p.cpp @@ -2,16 +2,16 @@ // 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 -#include -#include -#include -#include +#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; diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h index bb94db6..01d1230 100644 --- a/src/api/internal/BamMultiReader_p.h +++ b/src/api/internal/BamMultiReader_p.h @@ -2,7 +2,7 @@ // 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 // ************************************************************************* @@ -20,9 +20,9 @@ // // We mean it. -#include -#include -#include +#include "api/SamHeader.h" +#include "api/BamMultiReader.h" +#include "api/internal/BamMultiMerger_p.h" #include #include diff --git a/src/api/internal/BamPipe_p.cpp b/src/api/internal/BamPipe_p.cpp index 1d57ac3..e13ad7c 100644 --- a/src/api/internal/BamPipe_p.cpp +++ b/src/api/internal/BamPipe_p.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/internal/BamPipe_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamPipe_p.h b/src/api/internal/BamPipe_p.h index a9725be..8996766 100644 --- a/src/api/internal/BamPipe_p.h +++ b/src/api/internal/BamPipe_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/internal/ILocalIODevice_p.h" #include namespace BamTools { diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/BamRandomAccessController_p.cpp index a8b64b6..1e44b7d 100644 --- a/src/api/internal/BamRandomAccessController_p.cpp +++ b/src/api/internal/BamRandomAccessController_p.cpp @@ -2,16 +2,16 @@ // 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 -#include -#include -#include -#include +#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; diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/BamRandomAccessController_p.h index ff902b3..43b6fb0 100644 --- a/src/api/internal/BamRandomAccessController_p.h +++ b/src/api/internal/BamRandomAccessController_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,8 +20,8 @@ // // We mean it. -#include -#include +#include "api/BamAux.h" +#include "api/BamIndex.h" namespace BamTools { diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp index 393b168..11cba33 100644 --- a/src/api/internal/BamReader_p.cpp +++ b/src/api/internal/BamReader_p.cpp @@ -2,22 +2,21 @@ // 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 -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include +#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; diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/BamReader_p.h index ccc3835..2f670d5 100644 --- a/src/api/internal/BamReader_p.h +++ b/src/api/internal/BamReader_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,13 +20,13 @@ // // We mean it. -#include -#include -#include -#include -#include -#include -#include +#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 namespace BamTools { diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/BamStandardIndex_p.cpp index 6f280c2..c492899 100644 --- a/src/api/internal/BamStandardIndex_p.cpp +++ b/src/api/internal/BamStandardIndex_p.cpp @@ -2,15 +2,15 @@ // 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 -#include -#include -#include +#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; diff --git a/src/api/internal/BamStandardIndex_p.h b/src/api/internal/BamStandardIndex_p.h index 1bd36c8..cb907ac 100644 --- a/src/api/internal/BamStandardIndex_p.h +++ b/src/api/internal/BamStandardIndex_p.h @@ -2,7 +2,7 @@ // 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") // *************************************************************************** @@ -20,8 +20,8 @@ // // We mean it. -#include -#include +#include "api/BamAux.h" +#include "api/BamIndex.h" #include #include #include diff --git a/src/api/internal/BamToolsIndex_p.cpp b/src/api/internal/BamToolsIndex_p.cpp index 1142fbd..567b551 100644 --- a/src/api/internal/BamToolsIndex_p.cpp +++ b/src/api/internal/BamToolsIndex_p.cpp @@ -2,16 +2,16 @@ // 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 -#include -#include -#include -#include +#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; diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/BamToolsIndex_p.h index 96e35dc..902be79 100644 --- a/src/api/internal/BamToolsIndex_p.h +++ b/src/api/internal/BamToolsIndex_p.h @@ -2,7 +2,7 @@ // 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") // *************************************************************************** @@ -20,8 +20,8 @@ // // We mean it. -#include -#include +#include "api/BamAux.h" +#include "api/BamIndex.h" #include #include #include diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp index 28fbce7..1b1a3f2 100644 --- a/src/api/internal/BamWriter_p.cpp +++ b/src/api/internal/BamWriter_p.cpp @@ -2,16 +2,16 @@ // 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 -#include -#include -#include -#include +#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; @@ -160,7 +160,7 @@ bool BamWriterPrivate::Open(const string& filename, 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(); diff --git a/src/api/internal/BamWriter_p.h b/src/api/internal/BamWriter_p.h index e3547fe..cf10941 100644 --- a/src/api/internal/BamWriter_p.h +++ b/src/api/internal/BamWriter_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,8 +20,8 @@ // // We mean it. -#include -#include +#include "api/BamAux.h" +#include "api/internal/BgzfStream_p.h" #include #include diff --git a/src/api/internal/BgzfStream_p.cpp b/src/api/internal/BgzfStream_p.cpp index f70b97e..1744ddd 100644 --- a/src/api/internal/BgzfStream_p.cpp +++ b/src/api/internal/BgzfStream_p.cpp @@ -2,19 +2,23 @@ // 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 -#include -#include +#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 #include #include diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h index 0ad7a79..88d7472 100644 --- a/src/api/internal/BgzfStream_p.h +++ b/src/api/internal/BgzfStream_p.h @@ -2,7 +2,7 @@ // 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 @@ -22,12 +22,8 @@ // // We mean it. -#include -#include -#include -#include "zlib.h" -#include -#include +#include "api/api_global.h" +#include "api/IBamIODevice.h" #include namespace BamTools { diff --git a/src/api/internal/ILocalIODevice_p.cpp b/src/api/internal/ILocalIODevice_p.cpp index 279ab77..8730a91 100644 --- a/src/api/internal/ILocalIODevice_p.cpp +++ b/src/api/internal/ILocalIODevice_p.cpp @@ -2,12 +2,12 @@ // 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 +#include "api/internal/ILocalIODevice_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/ILocalIODevice_p.h b/src/api/internal/ILocalIODevice_p.h index 1e64899..a71f378 100644 --- a/src/api/internal/ILocalIODevice_p.h +++ b/src/api/internal/ILocalIODevice_p.h @@ -2,7 +2,7 @@ // 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 // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/IBamIODevice.h" namespace BamTools { namespace Internal { diff --git a/src/api/internal/SamFormatParser_p.cpp b/src/api/internal/SamFormatParser_p.cpp index b92e6fd..195fdcd 100644 --- a/src/api/internal/SamFormatParser_p.cpp +++ b/src/api/internal/SamFormatParser_p.cpp @@ -2,15 +2,15 @@ // 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 -#include -#include -#include +#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; diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/SamFormatPrinter_p.cpp index d81db5d..942a7af 100644 --- a/src/api/internal/SamFormatPrinter_p.cpp +++ b/src/api/internal/SamFormatPrinter_p.cpp @@ -2,14 +2,14 @@ // 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 -#include -#include +#include "api/SamConstants.h" +#include "api/SamHeader.h" +#include "api/internal/SamFormatPrinter_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/SamHeaderValidator_p.cpp b/src/api/internal/SamHeaderValidator_p.cpp index 75e2c13..094e79a 100644 --- a/src/api/internal/SamHeaderValidator_p.cpp +++ b/src/api/internal/SamHeaderValidator_p.cpp @@ -2,15 +2,15 @@ // 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 -#include -#include -#include +#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; diff --git a/src/api/internal/SamHeaderVersion_p.h b/src/api/internal/SamHeaderVersion_p.h index d166ca2..4f85df0 100644 --- a/src/api/internal/SamHeaderVersion_p.h +++ b/src/api/internal/SamHeaderVersion_p.h @@ -2,7 +2,7 @@ // 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 // ************************************************************************* @@ -20,7 +20,7 @@ // // We mean it. -#include +#include "api/SamConstants.h" #include #include diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt index e2a251b..0620b41 100644 --- a/src/toolkit/CMakeLists.txt +++ b/src/toolkit/CMakeLists.txt @@ -31,7 +31,7 @@ add_executable ( bamtools_cmd # 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 diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt index fab013a..46e7235 100644 --- a/src/utils/CMakeLists.txt +++ b/src/utils/CMakeLists.txt @@ -25,6 +25,6 @@ target_link_libraries ( BamTools-utils BamTools ) # set BamTools library properties set_target_properties( BamTools-utils PROPERTIES - SOVERSION 1.0.2 + SOVERSION 2.0.0 OUTPUT_NAME bamtools-utils ) diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp index 2e7a784..d3ad080 100644 --- a/src/utils/bamtools_fasta.cpp +++ b/src/utils/bamtools_fasta.cpp @@ -2,12 +2,12 @@ // 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 +#include "utils/bamtools_fasta.h" using namespace BamTools; #include diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h index 5cf85b3..c339943 100644 --- a/src/utils/bamtools_fasta.h +++ b/src/utils/bamtools_fasta.h @@ -2,7 +2,7 @@ // 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. // *************************************************************************** @@ -10,7 +10,7 @@ #ifndef BAMTOOLS_FASTA_H #define BAMTOOLS_FASTA_H -#include +#include "utils/utils_global.h" #include namespace BamTools { diff --git a/src/utils/bamtools_filter_engine.h b/src/utils/bamtools_filter_engine.h index ae1415d..2ece5e7 100644 --- a/src/utils/bamtools_filter_engine.h +++ b/src/utils/bamtools_filter_engine.h @@ -2,7 +2,7 @@ // 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 @@ -41,10 +41,11 @@ #ifndef BAMTOOLS_FILTER_ENGINE_H #define BAMTOOLS_FILTER_ENGINE_H -#include -#include -#include -#include +#include "utils/utils_global.h" +#include "utils/bamtools_filter_properties.h" +#include "utils/bamtools_filter_ruleparser.h" +#include "utils/bamtools_utilities.h" + #include #include #include diff --git a/src/utils/bamtools_filter_properties.h b/src/utils/bamtools_filter_properties.h index c810ba2..a69f31d 100644 --- a/src/utils/bamtools_filter_properties.h +++ b/src/utils/bamtools_filter_properties.h @@ -2,7 +2,7 @@ // 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 // @@ -39,9 +39,9 @@ #ifndef BAMTOOLS_FILTER_PROPERTIES_H #define BAMTOOLS_FILTER_PROPERTIES_H -#include -#include -#include +#include "utils/utils_global.h" +#include "utils/bamtools_utilities.h" +#include "utils/bamtools_variant.h" #include #include #include diff --git a/src/utils/bamtools_filter_ruleparser.h b/src/utils/bamtools_filter_ruleparser.h index 07328cb..f3079eb 100644 --- a/src/utils/bamtools_filter_ruleparser.h +++ b/src/utils/bamtools_filter_ruleparser.h @@ -2,7 +2,7 @@ // 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. // *************************************************************************** @@ -10,7 +10,7 @@ #ifndef BAMTOOLS_FILTER_RULEPARSER_H #define BAMTOOLS_FILTER_RULEPARSER_H -#include +#include "utils/bamtools_utilities.h" #include #include #include diff --git a/src/utils/bamtools_options.cpp b/src/utils/bamtools_options.cpp index 359018b..565c90e 100644 --- a/src/utils/bamtools_options.cpp +++ b/src/utils/bamtools_options.cpp @@ -2,7 +2,7 @@ // 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 // --------------------------------------------------------------------------- @@ -16,7 +16,7 @@ // * (BamTools namespace, added stdin/stdout) (DB) // *************************************************************************** -#include +#include "utils/bamtools_options.h" using namespace BamTools; #include diff --git a/src/utils/bamtools_options.h b/src/utils/bamtools_options.h index b49fd53..2afe129 100644 --- a/src/utils/bamtools_options.h +++ b/src/utils/bamtools_options.h @@ -2,7 +2,7 @@ // 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 // --------------------------------------------------------------------------- @@ -19,8 +19,8 @@ #ifndef BAMTOOLS_OPTIONS_H #define BAMTOOLS_OPTIONS_H -#include -#include +#include "utils/bamtools_variant.h" +#include "utils/utils_global.h" #include #include diff --git a/src/utils/bamtools_pileup_engine.cpp b/src/utils/bamtools_pileup_engine.cpp index e0a0ea9..0cdb4a5 100644 --- a/src/utils/bamtools_pileup_engine.cpp +++ b/src/utils/bamtools_pileup_engine.cpp @@ -2,12 +2,12 @@ // 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 +#include "utils/bamtools_pileup_engine.h" using namespace BamTools; #include diff --git a/src/utils/bamtools_pileup_engine.h b/src/utils/bamtools_pileup_engine.h index 24d7084..eeca56c 100644 --- a/src/utils/bamtools_pileup_engine.h +++ b/src/utils/bamtools_pileup_engine.h @@ -2,7 +2,7 @@ // 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. // *************************************************************************** @@ -10,8 +10,9 @@ #ifndef BAMTOOLS_PILEUP_ENGINE_H #define BAMTOOLS_PILEUP_ENGINE_H +#include "utils/utils_global.h" + #include -#include #include namespace BamTools { diff --git a/src/utils/bamtools_variant.h b/src/utils/bamtools_variant.h index 020b336..4c477fb 100644 --- a/src/utils/bamtools_variant.h +++ b/src/utils/bamtools_variant.h @@ -2,7 +2,7 @@ // 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 // --------------------------------------------------------------------------- @@ -17,7 +17,7 @@ #ifndef BAMTOOLS_VARIANT_H #define BAMTOOLS_VARIANT_H -#include +#include "utils/utils_global.h" #include #include #include