Cleaned up intra-API includes & moved version numbers to 2.0.0

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 88beb4edc1160c24e84af7dc43e8d1a72bc6fcc1..a04cf380cfff4cb9aac8d561d0fb28214b52e45a 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -30,9 +30,9 @@ ensure_out_of_source_build ("
 (or the Windows equivalent)\n")
 
 # set BamTools version information
 (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_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")
 
 # 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 9493c7fd5a1987f5e2c5715da2e2c5493bc7d6b9..61094123a734b527f709a6c7ea62e012b7330e93 100644 (file)
--- a/src/api/BamAlgorithms.h
+++ b/src/api/BamAlgorithms.h
@@ -12,7 +12,7 @@
 #ifndef BAMALGORITHMS_H
 #define BAMALGORITHMS_H
 
 #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
 
 /*! \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 d97c09f700195524e29cb421f672c9f7d4a02eaf..78d7d6b22b8801e374d168a4684ce06cca83d86b 100644 (file)
--- a/src/api/BamAlignment.cpp
+++ b/src/api/BamAlignment.cpp
@@ -7,8 +7,8 @@
 // Provides the BamAlignment data structure
 // ***************************************************************************
 
 // 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;
 
 using namespace BamTools;
 using namespace std;
 

diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h
index daea418228a7bf4759a946b8aa4d78d64278073f..9a8e7be0a7351a405317d6c0c281ad01c384a3c0 100644 (file)
--- a/src/api/BamAlignment.h
+++ b/src/api/BamAlignment.h
@@ -10,9 +10,9 @@
 #ifndef BAMALIGNMENT_H
 #define BAMALIGNMENT_H
 
 #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>
 #include <cstdlib>
 #include <cstring>
 #include <string>

diff --git a/src/api/BamAux.h b/src/api/BamAux.h
index 29a0209c06951f2db13367098432b2d59c98b932..f4511259ea67136934e736a3cebf0846353d65ed 100644 (file)
--- a/src/api/BamAux.h
+++ b/src/api/BamAux.h
@@ -10,7 +10,7 @@
 #ifndef BAMAUX_H\r
 #define BAMAUX_H\r
 \r
 #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
 #include <fstream> \r
 #include <iostream>\r
 #include <string>\r

diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h
index 7c115f1dfb96e08f3f1908d5125f56fcd643f57d..a94409680085a06ade138ceca8b78bfec431e609 100644 (file)
--- a/src/api/BamConstants.h
+++ b/src/api/BamConstants.h
@@ -10,7 +10,7 @@
 #ifndef BAM_CONSTANTS_H
 #define BAM_CONSTANTS_H
 
 #ifndef BAM_CONSTANTS_H
 #define BAM_CONSTANTS_H
 

-#include <api/api_global.h>
+#include "api/api_global.h"

 #include <cassert>
 #include <string>
 
 #include <cassert>
 #include <string>
 

diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h
index e967c09a5d7589514add01faf11274953e7fc1ea..5e40d87eb517d4fbc8797e8f5d874eb520602f56 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides basic BAM index interface
 // ***************************************************************************


@@ -10,8 +10,8 @@
 #ifndef BAM_INDEX_H
 #define BAM_INDEX_H
 
 #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 {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/BamMultiReader.cpp b/src/api/BamMultiReader.cpp
index 8712aadbb13cde63de00d792883edcc4cde23ce3..6efeff6047fb8ac2d6243f1c8eeef4c2e4580aba 100644 (file)
--- a/src/api/BamMultiReader.cpp
+++ b/src/api/BamMultiReader.cpp
@@ -12,8 +12,8 @@
 // precludes the need to sort merged files.
 // ***************************************************************************
 
 // 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>
 using namespace BamTools;
 
 #include <string>

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index 1b1c27021bc457962d17160b019619932d4ecee6..76d0810e2f6fa411b5cf00e80426304292c03d69 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Convenience class for reading multiple BAM files.
 // ***************************************************************************


@@ -10,8 +10,8 @@
 #ifndef BAMMULTIREADER_H
 #define BAMMULTIREADER_H
 
 #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>
 #include <map>
 #include <sstream>
 #include <string>

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 58a2f3fa6893c4c20c3edab6c121720083436b29..6e4a10f80ece0b7b6cfd0d55c125f6dd509bf012 100644 (file)
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -7,8 +7,8 @@
 // Provides read access to BAM files.
 // ***************************************************************************
 
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index 8e15a5c4abdb0e68804a035e1d3a116059c59ae0..30c4d5f4de1fa1c415738c54f914f9b7f5dd2314 100644 (file)
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -2,7 +2,7 @@
 // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
 // Marth Lab, Department of Biology, Boston College\r
 // ---------------------------------------------------------------------------\r
 // 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
 // ---------------------------------------------------------------------------\r
 // Provides read access to BAM files.\r
 // ***************************************************************************\r


@@ -10,10 +10,10 @@
 #ifndef BAMREADER_H\r
 #define BAMREADER_H\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
 #include <string>\r
 \r
 namespace BamTools {\r

diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp
index 4120ccb8fc02f2a2aa18a9d232fc600df562d242..b1582a86a8236ff4d9bca170b06a4148f4870dd5 100644 (file)
--- a/src/api/BamWriter.cpp
+++ b/src/api/BamWriter.cpp
@@ -7,10 +7,10 @@
 // Provides the basic functionality for producing BAM files\r
 // ***************************************************************************\r
 \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
 using namespace BamTools;\r
 using namespace BamTools::Internal;\r
 using namespace std;\r

diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h
index 6767a1cb9beafedb2f7f1795bb5a151dda0cf216..68257ee4a8a3e3145090154cd93fb601a1ca2666 100644 (file)
--- a/src/api/BamWriter.h
+++ b/src/api/BamWriter.h
@@ -10,8 +10,8 @@
 #ifndef BAMWRITER_H\r
 #define BAMWRITER_H\r
 \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
 #include <string>\r
 \r
 namespace BamTools {\r

diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
index 2ec006c3defaff5dabfe5af6fdba8b3baf8b45be..c85b71b740f532c6814442f2a6625ad20aacad14 100644 (file)
--- 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} )
 
 # 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
 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 5c1856ea4f97ab1b87d92c5fbedac77a5b6fb9a3..b34e449a04ed966756c8c1bc3cb71a60f7bd970f 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.)
 //
 // ---------------------------------------------------------------------------
 // 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
 
 #ifndef IBAMIODEVICE_H
 #define IBAMIODEVICE_H
 

-#include <api/api_global.h>
+#include "api/api_global.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/SamConstants.h b/src/api/SamConstants.h
index 913c21391cda75030a4b1bb9f190857730666faf..405668c796814fc3f911be1217d8912ea29dc1ff 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides constants for SAM header
 // ***************************************************************************


@@ -10,7 +10,7 @@
 #ifndef SAM_CONSTANTS_H
 #define SAM_CONSTANTS_H
 
 #ifndef SAM_CONSTANTS_H
 #define SAM_CONSTANTS_H
 

-#include <api/api_global.h>
+#include "api/api_global.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp
index c2ec0737f4c0f932920927456353769596193cdd..5de2abcd9006d6eb86693973c416b0a61b9b2998 100644 (file)
--- 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.
 // ***************************************************************************
 
 // 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;
 using namespace BamTools;
 using namespace BamTools::Internal;
 using namespace std;

diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h
index b5f37a67748d360e3b6784c2fe0ba798d3258420..50049947e627a29f5b077cb719b0c1a7874bb75a 100644 (file)
--- a/src/api/SamHeader.h
+++ b/src/api/SamHeader.h
@@ -10,10 +10,10 @@
 #ifndef SAM_HEADER_H
 #define SAM_HEADER_H
 
 #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>
 
 #include <string>
 #include <vector>
 

diff --git a/src/api/SamProgram.cpp b/src/api/SamProgram.cpp
index fed9b8b70dd833d102059c94c7b94211f48e0dbf..17206788eb60540fc7d7d12d3aed69349ede5055 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace std;
 

diff --git a/src/api/SamProgramChain.cpp b/src/api/SamProgramChain.cpp
index 8213402f99bb2d2fc31d1e9e68042897310ad715..88c218575dcbc8d3c56c9f4c03a23d1d14d554a1 100644 (file)
--- a/src/api/SamProgramChain.cpp
+++ b/src/api/SamProgramChain.cpp
@@ -7,7 +7,7 @@
 // Provides methods for operating on a SamProgram record "chain"
 // ***************************************************************************
 
 // Provides methods for operating on a SamProgram record "chain"
 // ***************************************************************************
 

-#include <api/SamProgramChain.h>
+#include "api/SamProgramChain.h"

 using namespace BamTools;
 
 #include <algorithm>
 using namespace BamTools;
 
 #include <algorithm>

diff --git a/src/api/SamProgramChain.h b/src/api/SamProgramChain.h
index 7e24e5e4b2b09f377c7fcefbd0ded82891de65e4..a2bd5322ae250df9e3cf193b2ffd0b2ab7e360fb 100644 (file)
--- a/src/api/SamProgramChain.h
+++ b/src/api/SamProgramChain.h
@@ -10,8 +10,8 @@
 #ifndef SAM_PROGRAMCHAIN_H
 #define SAM_PROGRAMCHAIN_H
 
 #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>
 
 #include <string>
 #include <vector>
 

diff --git a/src/api/SamReadGroup.cpp b/src/api/SamReadGroup.cpp
index a9170d7bee13854dc1116c0491c6fa2e5ac04e37..ce022ab5d3d84759f096fb5235abb31b0dc90b1d 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace std;
 

diff --git a/src/api/SamReadGroupDictionary.cpp b/src/api/SamReadGroupDictionary.cpp
index 724f302efb3b45176909b3c30050ed562a256ea1..c501773e58baa69455b59d8e06496c7d7d70a7ab 100644 (file)
--- a/src/api/SamReadGroupDictionary.cpp
+++ b/src/api/SamReadGroupDictionary.cpp
@@ -7,7 +7,7 @@
 // Provides methods for operating on a collection of SamReadGroup entries.
 // ***************************************************************************
 
 // Provides methods for operating on a collection of SamReadGroup entries.
 // ***************************************************************************
 

-#include <api/SamReadGroupDictionary.h>
+#include "api/SamReadGroupDictionary.h"

 using namespace BamTools;
 
 #include <algorithm>
 using namespace BamTools;
 
 #include <algorithm>

diff --git a/src/api/SamReadGroupDictionary.h b/src/api/SamReadGroupDictionary.h
index 89f23e0e4cab31ad0ef8c4be039e5ba5873f4f87..7a651e1501818c7d0c93ff30091ad68391f9fb82 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides methods for operating on a collection of SamReadGroup entries.
 // ***************************************************************************


@@ -10,8 +10,8 @@
 #ifndef SAM_READGROUP_DICTIONARY_H
 #define SAM_READGROUP_DICTIONARY_H
 
 #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>
 
 #include <string>
 #include <vector>
 

diff --git a/src/api/SamSequence.cpp b/src/api/SamSequence.cpp
index c8e375f8c87d00610436dbeb5bf3223fa9acdbf6..dea176bd1f5438ebcbf1c680d474546ab2042f67 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 #include <sstream>
 using namespace BamTools;
 using namespace std;

diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h
index aea59cc8945ab4d461dc693ac9cc779bf860a155..c1a8792065df16bdd1a10ba46f90b540ba7b6c95 100644 (file)
--- a/src/api/SamSequence.h
+++ b/src/api/SamSequence.h
@@ -10,7 +10,7 @@
 #ifndef SAM_SEQUENCE_H
 #define SAM_SEQUENCE_H
 
 #ifndef SAM_SEQUENCE_H
 #define SAM_SEQUENCE_H
 

-#include <api/api_global.h>
+#include "api/api_global.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/algorithms/Sort.h b/src/api/algorithms/Sort.h
index cf21479c82db87d3e51316a88d1c0808feabdffb..92cb165a2c44ac031c73c8142eae40fdd1f075d9 100644 (file)
--- a/src/api/algorithms/Sort.h
+++ b/src/api/algorithms/Sort.h
@@ -11,10 +11,10 @@
 #ifndef ALGORITHMS_SORT_H
 #define ALGORITHMS_SORT_H
 
 #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>
 #include <cassert>
 #include <algorithm>
 #include <functional>

diff --git a/src/api/internal/BamDeviceFactory_p.cpp b/src/api/internal/BamDeviceFactory_p.cpp
index da0daad6fb0f4ac1de636a1595de5279f28b9e5d..895d08c7516893f1a6e136ad49ddc857c43a3798 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamDeviceFactory_p.h b/src/api/internal/BamDeviceFactory_p.h
index f12683131a95bfd316fb1af3f811ba1ceafc2e90..1d48533d8687773384b4582f2e006a07612890eb 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Creates built-in concrete implementations of IBamIODevices
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamException_p.cpp b/src/api/internal/BamException_p.cpp
index 38241d88117c0d3c7994b4ce398b0ff1a7697a0a..38469e7109c25522ba7e96d63664acea92203fa0 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 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 3927d302879388516c1093eafe440f0ed963a3c9..74c4ed68d559d30aee7cf243fc8bc042b21bb5ea 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamFile_p.h b/src/api/internal/BamFile_p.h
index fd25a3e007787032c3bf0ec746de9e336a2bbf83..873e71ac39bbdddc49632bdfd0e30c48ef3aafec 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides BAM file-specific IO behavior
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/internal/ILocalIODevice_p.h>
+#include "api/internal/ILocalIODevice_p.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamFtp_p.cpp b/src/api/internal/BamFtp_p.cpp
index f9571970ea9fb9fb06c0cf9a7edcbf8db4391454..779d099b24d34c9867992634cd4d16db0b1658cb 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamFtp_p.h b/src/api/internal/BamFtp_p.h
index d410201c97529017dfc2637423721ce05055aa89..1f5ee0fdc9d1deed640d4439884b2d02e285ab1a 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides reading/writing of BAM files on FTP server
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamHeader_p.cpp b/src/api/internal/BamHeader_p.cpp
index 7ec1181703a07c8e7ad48bd4c2cf5b3c1f12d6f6..dc734bf619dd1e211768d2d4cabdb9c937dd4e51 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamHeader_p.h b/src/api/internal/BamHeader_p.h
index 42af68ce4f34dc1a4c2b70610469f2f2d9710d21..499ad96deaa15571c5235d946ecf2fe20bb8ad6d 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for handling BAM headers.
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/SamHeader.h>
+#include "api/SamHeader.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamHttp_p.cpp b/src/api/internal/BamHttp_p.cpp
index 532194ba1d9ab5060b341fe98815ac03365ee24e..83b4c3b4b98ec7d6f0ea5b1a76098bf493bea240 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamHttp_p.h b/src/api/internal/BamHttp_p.h
index e1d2403acbabb706325a765544a3341ce8f81542..38e94b7dcdd4e12ff7a8da8e7cb0bd70878bf514 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides reading/writing of BAM files on HTTP server
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/BamIndexFactory_p.cpp
index 4e9d1f28a4040aee6bc6140ffa23a61fad53f477..2cf871f9df8ec07650136e4178b7cf3f113b9114 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 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 7b1ff96a6425f42e717c800f55f839ea08ec5b09..4e4f1cfbf27cba533597930f93fccd17c384a98a 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides interface for generating BamIndex implementations
 // ***************************************************************************


@@ -10,7 +10,7 @@
 #ifndef BAMINDEX_FACTORY_P_H
 #define BAMINDEX_FACTORY_P_H
 
 #ifndef BAMINDEX_FACTORY_P_H
 #define BAMINDEX_FACTORY_P_H
 

-#include <api/BamIndex.h>
+#include "api/BamIndex.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/BamMultiMerger_p.h
index 2b7b110ad1ae4967ef086273f32650ea4fc6d848..3000097dd972e66456fb9eb7fffe668c9afbf054 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ---------------------------------------------------------------------------
 // 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.
 
 //
 // 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>
 #include <deque>
 #include <functional>
 #include <set>

diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/BamMultiReader_p.cpp
index f92258ddb856839d8c68721ae0af77990a8d101a..076f1bba9ac7e5a9e70d79a8e488f87e8f4fe2c2 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // *************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h
index bb94db620bd5b6d5d3fb55b387d77bdae14c4b63..01d12304f57c5ef6d113e07fc7ca7242a5c87e4f 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // *************************************************************************
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************


@@ -20,9 +20,9 @@
 //
 // We mean it.
 
 //
 // 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>
 
 #include <string>
 #include <vector>
 

diff --git a/src/api/internal/BamPipe_p.cpp b/src/api/internal/BamPipe_p.cpp
index 1d57ac35e03a675f66353b9115c232e27cabc4ee..e13ad7c759c6c1cce5870dfe83465fde1513836f 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamPipe_p.h b/src/api/internal/BamPipe_p.h
index a9725be7153bea5a08dbd221affe744bc903c55d..8996766f175e79859b709974fbcde1438c631806 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides BAM pipe-specific IO behavior
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/internal/ILocalIODevice_p.h>
+#include "api/internal/ILocalIODevice_p.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/BamRandomAccessController_p.cpp
index a8b64b6cfaf548460db8eeb0f99abddebd34151c..1e44b7daef47ccc52e96df28c6e1471b7e9cf270 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // **************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/BamRandomAccessController_p.h
index ff902b3077fd9bd73dcce70c8a2a26005de534b3..43b6fb038c18c196e78b79928e3f4de35d65425b 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Manages random access operations in a BAM file
 // ***************************************************************************


@@ -20,8 +20,8 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/BamAux.h>
-#include <api/BamIndex.h>
+#include "api/BamAux.h"
+#include "api/BamIndex.h"

 
 namespace BamTools {
 
 
 namespace BamTools {
 

diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp
index 393b168b74976a2f68b8d96dd47b39922be22d5d..11cba33ce177fabbc382738f99e6dcfb9b309554 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/BamReader_p.h
index ccc3835246a85b7372b1660be961339d5d4b8183..2f670d59d94d829aead92868f0ed8c7a13e2cec3 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for reading BAM files
 // ***************************************************************************


@@ -20,13 +20,13 @@
 //
 // We mean it.
 
 //
 // 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 {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/BamStandardIndex_p.cpp
index 6f280c2d1a1ebfaeb19e17e27ad1ba6c589345bb..c492899a20167d4924be71ff25d18c0b55fc0a18 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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")
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamStandardIndex_p.h b/src/api/internal/BamStandardIndex_p.h
index 1bd36c886e7a26a28d40c2df5e16ff40fe8c6758..cb907ac08a9f0cb623a452f87637515175274537 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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")
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides index operations for the standardized BAM index format (".bai")
 // ***************************************************************************


@@ -20,8 +20,8 @@
 //
 // We mean it.
 
 //
 // 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>
 #include <map>
 #include <set>
 #include <string>

diff --git a/src/api/internal/BamToolsIndex_p.cpp b/src/api/internal/BamToolsIndex_p.cpp
index 1142fbdbd0db958e7dab476c74ead9b5e3c3c06f..567b5514428d515348282f1bddfbfed14a55f7a9 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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")
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/BamToolsIndex_p.h
index 96e35dcb526fca9bd91037a03fd7d0c3031c997f..902be794295ad26bdb6fd35c8a52f5f1a69b974d 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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")
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides index operations for the BamTools index format (".bti")
 // ***************************************************************************


@@ -20,8 +20,8 @@
 //
 // We mean it.
 
 //
 // 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>
 #include <map>
 #include <string>
 #include <vector>

diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp
index 28fbce7c6755d3d3c197ae172dc387ad0aeb28bf..1b1a3f2136a4452e9a8509896b3c36c38b7873d7 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 


@@ -160,7 +160,7 @@ bool BamWriterPrivate::Open(const string& filename,
     try {
 
         // open the BGZF file for writing
     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();
 
         // write BAM file 'metadata' components
         WriteMagicNumber();

diff --git a/src/api/internal/BamWriter_p.h b/src/api/internal/BamWriter_p.h
index e3547fe43061ba1646090e0a2a9643a3ac85ad3a..cf109416b6f80c57866bd1d4fe518d31cd9e9826 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************


@@ -20,8 +20,8 @@
 //
 // We mean it.
 
 //
 // 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>
 
 #include <string>
 #include <vector>
 

diff --git a/src/api/internal/BgzfStream_p.cpp b/src/api/internal/BgzfStream_p.cpp
index f70b97eac1eb692035040ebf26a23bdc3686f75b..1744ddd37bf0bde872a41a8f60bbd117fc6634e3 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

+#include "zlib.h"
+

 #include <cstring>
 #include <algorithm>
 #include <iostream>
 #include <cstring>
 #include <algorithm>
 #include <iostream>

diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h
index 0ad7a793f0a8d8086ae3dcc54b943fc821166e7c..88d7472eeebfa81bed6cd2021841a2534877b7ac 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ---------------------------------------------------------------------------
 // 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.
 
 //
 // 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 {
 #include <string>
 
 namespace BamTools {

diff --git a/src/api/internal/ILocalIODevice_p.cpp b/src/api/internal/ILocalIODevice_p.cpp
index 279ab7787a3a99f1909e916b74a6321e83076658..8730a91505a02970887ed39ef050b30ba5528298 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/ILocalIODevice_p.h b/src/api/internal/ILocalIODevice_p.h
index 1e6489970dda6ef7a3f8baf904114ddc352f1516..a71f37896e10ad7b6c5186854d2a6b8b7d110135 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides shared behavior for files & pipes
 // ***************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/IBamIODevice.h>
+#include "api/IBamIODevice.h"

 
 namespace BamTools {
 namespace Internal {
 
 namespace BamTools {
 namespace Internal {

diff --git a/src/api/internal/SamFormatParser_p.cpp b/src/api/internal/SamFormatParser_p.cpp
index b92e6fdd0989fa0a5c874c9c009225a3c24482ef..195fdcd38b18336eb2344ff592b1d98c5a67d2fa 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/SamFormatPrinter_p.cpp
index d81db5d450918e4ca97ed04f5e8144b899b6ac4b..942a7af7bc9706d509ffc21123a66c5c91ca8dbe 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/SamHeaderValidator_p.cpp b/src/api/internal/SamHeaderValidator_p.cpp
index 75e2c135ff9f35ff1d929b800691af64d8dedb1c..094e79adb795ecb4a3560fab9700dce91ecbf80d 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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;
 
 using namespace BamTools;
 using namespace BamTools::Internal;
 

diff --git a/src/api/internal/SamHeaderVersion_p.h b/src/api/internal/SamHeaderVersion_p.h
index d166ca2e5fcc2b869226477ef9a252cecf71ee7d..4f85df0d231c6ef9d2590cf2c8669a59e98ca4f8 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // *************************************************************************
 // ---------------------------------------------------------------------------
 // Provides functionality for comparing SAM header versions
 // *************************************************************************


@@ -20,7 +20,7 @@
 //
 // We mean it.
 
 //
 // We mean it.
 

-#include <api/SamConstants.h>
+#include "api/SamConstants.h"

 #include <sstream>
 #include <string>
 
 #include <sstream>
 #include <string>
 

diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
index e2a251b5ddcc2e8b7084fd1c6ef8b11d3d352b6c..0620b41893a8b1997a2bdc178d9e52c341a34e9d 100644 (file)
--- 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
 
 # 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
                        OUTPUT_NAME "bamtools"
                      )
 # make version info available in application

diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt
index fab013a656264801caf75570d13b49a9f821f795..46e72352ef1005f4c8b2a3f4a2bb00442e2d2f13 100644 (file)
--- 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
 
 # set BamTools library properties
 set_target_properties( BamTools-utils PROPERTIES

-                       SOVERSION   1.0.2
+                       SOVERSION   2.0.0

                        OUTPUT_NAME bamtools-utils
                      )
                        OUTPUT_NAME bamtools-utils
                      )

diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp
index 2e7a784d9f606684d7854ba2eb1b7cef7cb60032..d3ad080926c8c4418cd2542ca9d69583049b598a 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // Provides FASTA reading/indexing functionality.
 // ***************************************************************************
 

-#include <utils/bamtools_fasta.h>
+#include "utils/bamtools_fasta.h"

 using namespace BamTools;
 
 #include <cstdio>
 using namespace BamTools;
 
 #include <cstdio>

diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h
index 5cf85b356761f0bc6b0830bfa83f13bee05846f9..c339943c3259c221255bf93d1e4c778785c26bc1 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides FASTA reading/indexing functionality.
 // ***************************************************************************


@@ -10,7 +10,7 @@
 #ifndef BAMTOOLS_FASTA_H
 #define BAMTOOLS_FASTA_H
 
 #ifndef BAMTOOLS_FASTA_H
 #define BAMTOOLS_FASTA_H
 

-#include <utils/utils_global.h>
+#include "utils/utils_global.h"

 #include <string>
 
 namespace BamTools {
 #include <string>
 
 namespace BamTools {

diff --git a/src/utils/bamtools_filter_engine.h b/src/utils/bamtools_filter_engine.h
index ae1415d8e90e9b37907277e21ee2e821e4f33a2d..2ece5e71e1e7b1206cec758892c6d074a2270855 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ---------------------------------------------------------------------------
 // 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
 
 #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>
 #include <algorithm>
 #include <iostream>
 #include <map>

diff --git a/src/utils/bamtools_filter_properties.h b/src/utils/bamtools_filter_properties.h
index c810ba24c5a20b47570a73f13890ca79801ccd68..a69f31d643f558ec58208d7054585005374a1eaf 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 //
 // ---------------------------------------------------------------------------
 // Provides support data structures & methods for FilterEngine
 //


@@ -39,9 +39,9 @@
 #ifndef BAMTOOLS_FILTER_PROPERTIES_H
 #define BAMTOOLS_FILTER_PROPERTIES_H
 
 #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>
 #include <iostream>
 #include <map>
 #include <string>

diff --git a/src/utils/bamtools_filter_ruleparser.h b/src/utils/bamtools_filter_ruleparser.h
index 07328cb4b89e5852e395516358f9fb0f2328c798..f3079eb561708af09db1ada331d7c9c1fcd8c47c 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides a compound rule parser for FilterEngine.
 // ***************************************************************************


@@ -10,7 +10,7 @@
 #ifndef BAMTOOLS_FILTER_RULEPARSER_H
 #define BAMTOOLS_FILTER_RULEPARSER_H
 
 #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>
 #include <queue>
 #include <stack>
 #include <string>

diff --git a/src/utils/bamtools_options.cpp b/src/utils/bamtools_options.cpp
index 359018b3b788f14d5ef277644061999a6907051a..565c90e56cdacb1084b6895505947393f788d3e1 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ---------------------------------------------------------------------------
 // ---------------------------------------------------------------------------
 // Parses command line arguments and creates a help menu
 // ---------------------------------------------------------------------------


@@ -16,7 +16,7 @@
 // *  (BamTools namespace, added stdin/stdout) (DB)
 // ***************************************************************************
 
 // *  (BamTools namespace, added stdin/stdout) (DB)
 // ***************************************************************************
 

-#include <utils/bamtools_options.h>
+#include "utils/bamtools_options.h"

 using namespace BamTools;
 
 #include <cstdio>
 using namespace BamTools;
 
 #include <cstdio>

diff --git a/src/utils/bamtools_options.h b/src/utils/bamtools_options.h
index b49fd535a432f47eb64a82b053a681e794fdfcfb..2afe1297661e80cdff94c4dd75631df1b97302d5 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ---------------------------------------------------------------------------
 // ---------------------------------------------------------------------------
 // Parses command line arguments and creates a help menu
 // ---------------------------------------------------------------------------


@@ -19,8 +19,8 @@
 #ifndef BAMTOOLS_OPTIONS_H
 #define BAMTOOLS_OPTIONS_H
 
 #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>
 
 #include <map>
 #include <string>

diff --git a/src/utils/bamtools_pileup_engine.cpp b/src/utils/bamtools_pileup_engine.cpp
index e0a0ea98c5cbddbda7582b4675382eebba93cdbf..0cdb4a571bdcb93c5f12ab6e37b42f9052e1a6b5 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 
 // ---------------------------------------------------------------------------
 // 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>
 using namespace BamTools;
 
 #include <iostream>

diff --git a/src/utils/bamtools_pileup_engine.h b/src/utils/bamtools_pileup_engine.h
index 24d70849e16fd1ab8eccb137dd15573f853d80b0..eeca56c85f1c6da220b4ebb3e0b1d03632b50fa3 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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.
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides pileup at position functionality for various tools.
 // ***************************************************************************


@@ -10,8 +10,9 @@
 #ifndef BAMTOOLS_PILEUP_ENGINE_H
 #define BAMTOOLS_PILEUP_ENGINE_H
 
 #ifndef BAMTOOLS_PILEUP_ENGINE_H
 #define BAMTOOLS_PILEUP_ENGINE_H
 

+#include "utils/utils_global.h"
+

 #include <api/BamAlignment.h>
 #include <api/BamAlignment.h>

-#include <utils/utils_global.h>

 #include <vector>
 
 namespace BamTools {
 #include <vector>
 
 namespace BamTools {

diff --git a/src/utils/bamtools_variant.h b/src/utils/bamtools_variant.h
index 020b3363baa1a316d4bea7a6fa75e1901c7a953f..4c477fb253829c827bcab6c3bb4c1c1cfb424aff 100644 (file)
--- 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
 // ---------------------------------------------------------------------------
 // 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
 // ---------------------------------------------------------------------------
 // ---------------------------------------------------------------------------
 // Provides a template-based variant type
 // ---------------------------------------------------------------------------


@@ -17,7 +17,7 @@
 #ifndef BAMTOOLS_VARIANT_H
 #define BAMTOOLS_VARIANT_H
 
 #ifndef BAMTOOLS_VARIANT_H
 #define BAMTOOLS_VARIANT_H
 

-#include <utils/utils_global.h>
+#include "utils/utils_global.h"

 #include <stdexcept>
 #include <string>
 #include <typeinfo>
 #include <stdexcept>
 #include <string>
 #include <typeinfo>