From 90432a3736392f98803a5e8787f3db0dc5bb44ad Mon Sep 17 00:00:00 2001 From: derek Date: Tue, 25 Oct 2011 12:33:54 -0400 Subject: [PATCH] Organized api/internal into subdirs --- src/api/BamMultiReader.cpp | 4 +- src/api/BamMultiReader.h | 2 +- src/api/BamReader.cpp | 4 +- src/api/BamWriter.cpp | 4 +- src/api/CMakeLists.txt | 40 +++++++++---------- src/api/SamHeader.cpp | 10 ++--- src/api/internal/{ => bam}/BamHeader_p.cpp | 8 ++-- src/api/internal/{ => bam}/BamHeader_p.h | 0 src/api/internal/{ => bam}/BamMultiMerger_p.h | 0 .../internal/{ => bam}/BamMultiReader_p.cpp | 4 +- src/api/internal/{ => bam}/BamMultiReader_p.h | 4 +- .../{ => bam}/BamRandomAccessController_p.cpp | 10 ++--- .../{ => bam}/BamRandomAccessController_p.h | 0 src/api/internal/{ => bam}/BamReader_p.cpp | 16 ++++---- src/api/internal/{ => bam}/BamReader_p.h | 8 ++-- src/api/internal/{ => bam}/BamWriter_p.cpp | 6 +-- src/api/internal/{ => bam}/BamWriter_p.h | 4 +- .../{ => index}/BamIndexFactory_p.cpp | 8 ++-- .../internal/{ => index}/BamIndexFactory_p.h | 0 .../{ => index}/BamStandardIndex_p.cpp | 8 ++-- .../internal/{ => index}/BamStandardIndex_p.h | 0 .../internal/{ => index}/BamToolsIndex_p.cpp | 10 ++--- .../internal/{ => index}/BamToolsIndex_p.h | 0 .../internal/{ => io}/BamDeviceFactory_p.cpp | 12 +++--- .../internal/{ => io}/BamDeviceFactory_p.h | 0 src/api/internal/{ => io}/BamFile_p.cpp | 4 +- src/api/internal/{ => io}/BamFile_p.h | 4 +- src/api/internal/{ => io}/BamFtp_p.cpp | 4 +- src/api/internal/{ => io}/BamFtp_p.h | 0 src/api/internal/{ => io}/BamHttp_p.cpp | 4 +- src/api/internal/{ => io}/BamHttp_p.h | 0 src/api/internal/{ => io}/BamPipe_p.cpp | 4 +- src/api/internal/{ => io}/BamPipe_p.h | 4 +- src/api/internal/{ => io}/BgzfStream_p.cpp | 8 ++-- src/api/internal/{ => io}/BgzfStream_p.h | 0 .../internal/{ => io}/ILocalIODevice_p.cpp | 4 +- src/api/internal/{ => io}/ILocalIODevice_p.h | 0 .../internal/{ => io}/IRemoteIODevice_p.cpp | 0 src/api/internal/{ => io}/IRemoteIODevice_p.h | 0 .../internal/{ => sam}/SamFormatParser_p.cpp | 6 +-- .../internal/{ => sam}/SamFormatParser_p.h | 0 .../internal/{ => sam}/SamFormatPrinter_p.cpp | 4 +- .../internal/{ => sam}/SamFormatPrinter_p.h | 0 .../{ => sam}/SamHeaderValidator_p.cpp | 6 +-- .../internal/{ => sam}/SamHeaderValidator_p.h | 0 .../internal/{ => sam}/SamHeaderVersion_p.h | 0 .../internal/{ => utils}/BamException_p.cpp | 4 +- src/api/internal/{ => utils}/BamException_p.h | 0 48 files changed, 109 insertions(+), 109 deletions(-) rename src/api/internal/{ => bam}/BamHeader_p.cpp (95%) rename src/api/internal/{ => bam}/BamHeader_p.h (100%) rename src/api/internal/{ => bam}/BamMultiMerger_p.h (100%) rename src/api/internal/{ => bam}/BamMultiReader_p.cpp (99%) rename src/api/internal/{ => bam}/BamMultiReader_p.h (97%) rename src/api/internal/{ => bam}/BamRandomAccessController_p.cpp (97%) rename src/api/internal/{ => bam}/BamRandomAccessController_p.h (100%) rename src/api/internal/{ => bam}/BamReader_p.cpp (97%) rename src/api/internal/{ => bam}/BamReader_p.h (95%) rename src/api/internal/{ => bam}/BamWriter_p.cpp (99%) rename src/api/internal/{ => bam}/BamWriter_p.h (96%) rename src/api/internal/{ => index}/BamIndexFactory_p.cpp (95%) rename src/api/internal/{ => index}/BamIndexFactory_p.h (100%) rename src/api/internal/{ => index}/BamStandardIndex_p.cpp (99%) rename src/api/internal/{ => index}/BamStandardIndex_p.h (100%) rename src/api/internal/{ => index}/BamToolsIndex_p.cpp (99%) rename src/api/internal/{ => index}/BamToolsIndex_p.h (100%) rename src/api/internal/{ => io}/BamDeviceFactory_p.cpp (81%) rename src/api/internal/{ => io}/BamDeviceFactory_p.h (100%) rename src/api/internal/{ => io}/BamFile_p.cpp (96%) rename src/api/internal/{ => io}/BamFile_p.h (93%) rename src/api/internal/{ => io}/BamFtp_p.cpp (94%) rename src/api/internal/{ => io}/BamFtp_p.h (100%) rename src/api/internal/{ => io}/BamHttp_p.cpp (94%) rename src/api/internal/{ => io}/BamHttp_p.h (100%) rename src/api/internal/{ => io}/BamPipe_p.cpp (95%) rename src/api/internal/{ => io}/BamPipe_p.h (93%) rename src/api/internal/{ => io}/BgzfStream_p.cpp (98%) rename src/api/internal/{ => io}/BgzfStream_p.h (100%) rename src/api/internal/{ => io}/ILocalIODevice_p.cpp (95%) rename src/api/internal/{ => io}/ILocalIODevice_p.h (100%) rename src/api/internal/{ => io}/IRemoteIODevice_p.cpp (100%) rename src/api/internal/{ => io}/IRemoteIODevice_p.h (100%) rename src/api/internal/{ => sam}/SamFormatParser_p.cpp (98%) rename src/api/internal/{ => sam}/SamFormatParser_p.h (100%) rename src/api/internal/{ => sam}/SamFormatPrinter_p.cpp (98%) rename src/api/internal/{ => sam}/SamFormatPrinter_p.h (100%) rename src/api/internal/{ => sam}/SamHeaderValidator_p.cpp (99%) rename src/api/internal/{ => sam}/SamHeaderValidator_p.h (100%) rename src/api/internal/{ => sam}/SamHeaderVersion_p.h (100%) rename src/api/internal/{ => utils}/BamException_p.cpp (87%) rename src/api/internal/{ => utils}/BamException_p.h (100%) diff --git a/src/api/BamMultiReader.cpp b/src/api/BamMultiReader.cpp index ef38469..f61aa26 100644 --- a/src/api/BamMultiReader.cpp +++ b/src/api/BamMultiReader.cpp @@ -2,7 +2,7 @@ // BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Convenience class for reading multiple BAM files. // @@ -13,7 +13,7 @@ // *************************************************************************** #include "api/BamMultiReader.h" -#include "api/internal/BamMultiReader_p.h" +#include "api/internal/bam/BamMultiReader_p.h" using namespace BamTools; #include diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h index ea068d0..e5fc9c9 100644 --- a/src/api/BamMultiReader.h +++ b/src/api/BamMultiReader.h @@ -2,7 +2,7 @@ // BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Convenience class for reading multiple BAM files. // *************************************************************************** diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp index 6080b36..ae2adec 100644 --- a/src/api/BamReader.cpp +++ b/src/api/BamReader.cpp @@ -2,13 +2,13 @@ // BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides read access to BAM files. // *************************************************************************** #include "api/BamReader.h" -#include "api/internal/BamReader_p.h" +#include "api/internal/bam/BamReader_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp index b1582a8..cbbfdae 100644 --- a/src/api/BamWriter.cpp +++ b/src/api/BamWriter.cpp @@ -2,7 +2,7 @@ // BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for producing BAM files // *************************************************************************** @@ -10,7 +10,7 @@ #include "api/BamAlignment.h" #include "api/BamWriter.h" #include "api/SamHeader.h" -#include "api/internal/BamWriter_p.h" +#include "api/internal/bam/BamWriter_p.h" using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt index 55f2560..d6a5b10 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@ -25,26 +25,26 @@ set( BamToolsAPISources SamReadGroupDictionary.cpp SamSequence.cpp SamSequenceDictionary.cpp - internal/BamDeviceFactory_p.cpp - internal/BamException_p.cpp - internal/BamFile_p.cpp - internal/BamFtp_p.cpp - internal/BamHeader_p.cpp - internal/BamHttp_p.cpp - internal/BamIndexFactory_p.cpp - internal/BamMultiReader_p.cpp - internal/BamPipe_p.cpp - internal/BamRandomAccessController_p.cpp - internal/BamReader_p.cpp - internal/BamStandardIndex_p.cpp - internal/BamToolsIndex_p.cpp - internal/BamWriter_p.cpp - internal/BgzfStream_p.cpp - internal/ILocalIODevice_p.cpp - internal/IRemoteIODevice_p.cpp - internal/SamFormatParser_p.cpp - internal/SamFormatPrinter_p.cpp - internal/SamHeaderValidator_p.cpp + internal/bam/BamHeader_p.cpp + internal/bam/BamMultiReader_p.cpp + internal/bam/BamRandomAccessController_p.cpp + internal/bam/BamReader_p.cpp + internal/bam/BamWriter_p.cpp + internal/index/BamIndexFactory_p.cpp + internal/index/BamStandardIndex_p.cpp + internal/index/BamToolsIndex_p.cpp + internal/io/BamDeviceFactory_p.cpp + internal/io/BamFile_p.cpp + internal/io/BamFtp_p.cpp + internal/io/BamHttp_p.cpp + internal/io/BamPipe_p.cpp + internal/io/BgzfStream_p.cpp + internal/io/ILocalIODevice_p.cpp + internal/io/IRemoteIODevice_p.cpp + internal/sam/SamFormatParser_p.cpp + internal/sam/SamFormatPrinter_p.cpp + internal/sam/SamHeaderValidator_p.cpp + internal/utils/BamException_p.cpp ) # create main BamTools API shared library diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp index 5de2abc..b2925f2 100644 --- a/src/api/SamHeader.cpp +++ b/src/api/SamHeader.cpp @@ -2,17 +2,17 @@ // SamHeader.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // 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/internal/utils/BamException_p.h" +#include "api/internal/sam/SamFormatParser_p.h" +#include "api/internal/sam/SamFormatPrinter_p.h" +#include "api/internal/sam/SamHeaderValidator_p.h" using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/internal/BamHeader_p.cpp b/src/api/internal/bam/BamHeader_p.cpp similarity index 95% rename from src/api/internal/BamHeader_p.cpp rename to src/api/internal/bam/BamHeader_p.cpp index dc734bf..02c0a25 100644 --- a/src/api/internal/BamHeader_p.cpp +++ b/src/api/internal/bam/BamHeader_p.cpp @@ -2,16 +2,16 @@ // BamHeader_p.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for handling BAM headers. // *************************************************************************** #include "api/BamAux.h" #include "api/BamConstants.h" -#include "api/internal/BamException_p.h" -#include "api/internal/BamHeader_p.h" -#include "api/internal/BgzfStream_p.h" +#include "api/internal/bam/BamHeader_p.h" +#include "api/internal/io/BgzfStream_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamHeader_p.h b/src/api/internal/bam/BamHeader_p.h similarity index 100% rename from src/api/internal/BamHeader_p.h rename to src/api/internal/bam/BamHeader_p.h diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/bam/BamMultiMerger_p.h similarity index 100% rename from src/api/internal/BamMultiMerger_p.h rename to src/api/internal/bam/BamMultiMerger_p.h diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/bam/BamMultiReader_p.cpp similarity index 99% rename from src/api/internal/BamMultiReader_p.cpp rename to src/api/internal/bam/BamMultiReader_p.cpp index 55ae615..d3f2b15 100644 --- a/src/api/internal/BamMultiReader_p.cpp +++ b/src/api/internal/bam/BamMultiReader_p.cpp @@ -2,7 +2,7 @@ // BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 14 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Functionality for simultaneously reading multiple BAM files // ************************************************************************* @@ -11,7 +11,7 @@ #include "api/BamMultiReader.h" #include "api/SamConstants.h" #include "api/algorithms/Sort.h" -#include "api/internal/BamMultiReader_p.h" +#include "api/internal/bam/BamMultiReader_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/bam/BamMultiReader_p.h similarity index 97% rename from src/api/internal/BamMultiReader_p.h rename to src/api/internal/bam/BamMultiReader_p.h index 9d001f5..9d7c39a 100644 --- a/src/api/internal/BamMultiReader_p.h +++ b/src/api/internal/bam/BamMultiReader_p.h @@ -2,7 +2,7 @@ // BamMultiReader_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Functionality for simultaneously reading multiple BAM files // ************************************************************************* @@ -22,7 +22,7 @@ #include "api/SamHeader.h" #include "api/BamMultiReader.h" -#include "api/internal/BamMultiMerger_p.h" +#include "api/internal/bam/BamMultiMerger_p.h" #include #include diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/bam/BamRandomAccessController_p.cpp similarity index 97% rename from src/api/internal/BamRandomAccessController_p.cpp rename to src/api/internal/bam/BamRandomAccessController_p.cpp index c223ed7..848fafd 100644 --- a/src/api/internal/BamRandomAccessController_p.cpp +++ b/src/api/internal/bam/BamRandomAccessController_p.cpp @@ -2,16 +2,16 @@ // BamRandomAccessController_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011(DB) +// Last modified: 25 October 2011(DB) // --------------------------------------------------------------------------- // Manages random access operations in a BAM file // ************************************************************************** #include "api/BamIndex.h" -#include "api/internal/BamException_p.h" -#include "api/internal/BamRandomAccessController_p.h" -#include "api/internal/BamReader_p.h" -#include "api/internal/BamIndexFactory_p.h" +#include "api/internal/bam/BamRandomAccessController_p.h" +#include "api/internal/bam/BamReader_p.h" +#include "api/internal/index/BamIndexFactory_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/bam/BamRandomAccessController_p.h similarity index 100% rename from src/api/internal/BamRandomAccessController_p.h rename to src/api/internal/bam/BamRandomAccessController_p.h diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/bam/BamReader_p.cpp similarity index 97% rename from src/api/internal/BamReader_p.cpp rename to src/api/internal/bam/BamReader_p.cpp index dc6792f..6484a10 100644 --- a/src/api/internal/BamReader_p.cpp +++ b/src/api/internal/bam/BamReader_p.cpp @@ -2,7 +2,7 @@ // BamReader_p.cpp (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for reading BAM files // *************************************************************************** @@ -10,13 +10,13 @@ #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/bam/BamHeader_p.h" +#include "api/internal/bam/BamRandomAccessController_p.h" +#include "api/internal/bam/BamReader_p.h" +#include "api/internal/index/BamStandardIndex_p.h" +#include "api/internal/index/BamToolsIndex_p.h" +#include "api/internal/io/BamDeviceFactory_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/bam/BamReader_p.h similarity index 95% rename from src/api/internal/BamReader_p.h rename to src/api/internal/bam/BamReader_p.h index f928273..e8db646 100644 --- a/src/api/internal/BamReader_p.h +++ b/src/api/internal/bam/BamReader_p.h @@ -2,7 +2,7 @@ // BamReader_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for reading BAM files // *************************************************************************** @@ -24,9 +24,9 @@ #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/internal/bam/BamHeader_p.h" +#include "api/internal/bam/BamRandomAccessController_p.h" +#include "api/internal/io/BgzfStream_p.h" #include namespace BamTools { diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/bam/BamWriter_p.cpp similarity index 99% rename from src/api/internal/BamWriter_p.cpp rename to src/api/internal/bam/BamWriter_p.cpp index 1b1a3f2..ba4989f 100644 --- a/src/api/internal/BamWriter_p.cpp +++ b/src/api/internal/bam/BamWriter_p.cpp @@ -2,7 +2,7 @@ // BamWriter_p.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for producing BAM files // *************************************************************************** @@ -10,8 +10,8 @@ #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/internal/bam/BamWriter_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamWriter_p.h b/src/api/internal/bam/BamWriter_p.h similarity index 96% rename from src/api/internal/BamWriter_p.h rename to src/api/internal/bam/BamWriter_p.h index cf10941..d5bbe8d 100644 --- a/src/api/internal/BamWriter_p.h +++ b/src/api/internal/bam/BamWriter_p.h @@ -2,7 +2,7 @@ // BamWriter_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for producing BAM files // *************************************************************************** @@ -21,7 +21,7 @@ // We mean it. #include "api/BamAux.h" -#include "api/internal/BgzfStream_p.h" +#include "api/internal/io/BgzfStream_p.h" #include #include diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/index/BamIndexFactory_p.cpp similarity index 95% rename from src/api/internal/BamIndexFactory_p.cpp rename to src/api/internal/index/BamIndexFactory_p.cpp index 2cf871f..3afcbb9 100644 --- a/src/api/internal/BamIndexFactory_p.cpp +++ b/src/api/internal/index/BamIndexFactory_p.cpp @@ -2,15 +2,15 @@ // BamIndexFactory_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides interface for generating BamIndex implementations // *************************************************************************** #include "api/BamAux.h" -#include "api/internal/BamIndexFactory_p.h" -#include "api/internal/BamStandardIndex_p.h" -#include "api/internal/BamToolsIndex_p.h" +#include "api/internal/index/BamIndexFactory_p.h" +#include "api/internal/index/BamStandardIndex_p.h" +#include "api/internal/index/BamToolsIndex_p.h" using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/internal/BamIndexFactory_p.h b/src/api/internal/index/BamIndexFactory_p.h similarity index 100% rename from src/api/internal/BamIndexFactory_p.h rename to src/api/internal/index/BamIndexFactory_p.h diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/index/BamStandardIndex_p.cpp similarity index 99% rename from src/api/internal/BamStandardIndex_p.cpp rename to src/api/internal/index/BamStandardIndex_p.cpp index 8b23f74..706c7c1 100644 --- a/src/api/internal/BamStandardIndex_p.cpp +++ b/src/api/internal/index/BamStandardIndex_p.cpp @@ -2,15 +2,15 @@ // BamStandardIndex.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides index operations for the standardized BAM index format (".bai") // *************************************************************************** #include "api/BamAlignment.h" -#include "api/internal/BamException_p.h" -#include "api/internal/BamReader_p.h" -#include "api/internal/BamStandardIndex_p.h" +#include "api/internal/bam/BamReader_p.h" +#include "api/internal/index/BamStandardIndex_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamStandardIndex_p.h b/src/api/internal/index/BamStandardIndex_p.h similarity index 100% rename from src/api/internal/BamStandardIndex_p.h rename to src/api/internal/index/BamStandardIndex_p.h diff --git a/src/api/internal/BamToolsIndex_p.cpp b/src/api/internal/index/BamToolsIndex_p.cpp similarity index 99% rename from src/api/internal/BamToolsIndex_p.cpp rename to src/api/internal/index/BamToolsIndex_p.cpp index cdf3d10..af0a684 100644 --- a/src/api/internal/BamToolsIndex_p.cpp +++ b/src/api/internal/index/BamToolsIndex_p.cpp @@ -2,16 +2,16 @@ // BamToolsIndex.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides index operations for the BamTools index format (".bti") // *************************************************************************** #include "api/BamAlignment.h" -#include "api/internal/BamException_p.h" -#include "api/internal/BamReader_p.h" -#include "api/internal/BamToolsIndex_p.h" -#include "api/internal/BgzfStream_p.h" +#include "api/internal/bam/BamReader_p.h" +#include "api/internal/index/BamToolsIndex_p.h" +#include "api/internal/io/BgzfStream_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/index/BamToolsIndex_p.h similarity index 100% rename from src/api/internal/BamToolsIndex_p.h rename to src/api/internal/index/BamToolsIndex_p.h diff --git a/src/api/internal/BamDeviceFactory_p.cpp b/src/api/internal/io/BamDeviceFactory_p.cpp similarity index 81% rename from src/api/internal/BamDeviceFactory_p.cpp rename to src/api/internal/io/BamDeviceFactory_p.cpp index 895d08c..f9c7694 100644 --- a/src/api/internal/BamDeviceFactory_p.cpp +++ b/src/api/internal/io/BamDeviceFactory_p.cpp @@ -2,16 +2,16 @@ // BamDeviceFactory_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 September 2011 (DB) +// Last modified: 25 September 2011 (DB) // --------------------------------------------------------------------------- // Creates built-in concrete implementations of IBamIODevices // *************************************************************************** -#include "api/internal/BamDeviceFactory_p.h" -#include "api/internal/BamFile_p.h" -#include "api/internal/BamFtp_p.h" -#include "api/internal/BamHttp_p.h" -#include "api/internal/BamPipe_p.h" +#include "api/internal/io/BamDeviceFactory_p.h" +#include "api/internal/io/BamFile_p.h" +#include "api/internal/io/BamFtp_p.h" +#include "api/internal/io/BamHttp_p.h" +#include "api/internal/io/BamPipe_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamDeviceFactory_p.h b/src/api/internal/io/BamDeviceFactory_p.h similarity index 100% rename from src/api/internal/BamDeviceFactory_p.h rename to src/api/internal/io/BamDeviceFactory_p.h diff --git a/src/api/internal/BamFile_p.cpp b/src/api/internal/io/BamFile_p.cpp similarity index 96% rename from src/api/internal/BamFile_p.cpp rename to src/api/internal/io/BamFile_p.cpp index 74c4ed6..94c919e 100644 --- a/src/api/internal/BamFile_p.cpp +++ b/src/api/internal/io/BamFile_p.cpp @@ -2,12 +2,12 @@ // BamFile_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides BAM file-specific IO behavior // *************************************************************************** -#include "api/internal/BamFile_p.h" +#include "api/internal/io/BamFile_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamFile_p.h b/src/api/internal/io/BamFile_p.h similarity index 93% rename from src/api/internal/BamFile_p.h rename to src/api/internal/io/BamFile_p.h index 873e71a..bd7d64b 100644 --- a/src/api/internal/BamFile_p.h +++ b/src/api/internal/io/BamFile_p.h @@ -2,7 +2,7 @@ // BamFile_p.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides BAM file-specific IO behavior // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include "api/internal/ILocalIODevice_p.h" +#include "api/internal/io/ILocalIODevice_p.h" #include namespace BamTools { diff --git a/src/api/internal/BamFtp_p.cpp b/src/api/internal/io/BamFtp_p.cpp similarity index 94% rename from src/api/internal/BamFtp_p.cpp rename to src/api/internal/io/BamFtp_p.cpp index 779d099..f94d4ac 100644 --- a/src/api/internal/BamFtp_p.cpp +++ b/src/api/internal/io/BamFtp_p.cpp @@ -2,12 +2,12 @@ // BamFtp_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides reading/writing of BAM files on FTP server // *************************************************************************** -#include "api/internal/BamFtp_p.h" +#include "api/internal/io/BamFtp_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamFtp_p.h b/src/api/internal/io/BamFtp_p.h similarity index 100% rename from src/api/internal/BamFtp_p.h rename to src/api/internal/io/BamFtp_p.h diff --git a/src/api/internal/BamHttp_p.cpp b/src/api/internal/io/BamHttp_p.cpp similarity index 94% rename from src/api/internal/BamHttp_p.cpp rename to src/api/internal/io/BamHttp_p.cpp index 83b4c3b..2892829 100644 --- a/src/api/internal/BamHttp_p.cpp +++ b/src/api/internal/io/BamHttp_p.cpp @@ -2,12 +2,12 @@ // BamHttp_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides reading/writing of BAM files on HTTP server // *************************************************************************** -#include "api/internal/BamHttp_p.h" +#include "api/internal/io/BamHttp_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamHttp_p.h b/src/api/internal/io/BamHttp_p.h similarity index 100% rename from src/api/internal/BamHttp_p.h rename to src/api/internal/io/BamHttp_p.h diff --git a/src/api/internal/BamPipe_p.cpp b/src/api/internal/io/BamPipe_p.cpp similarity index 95% rename from src/api/internal/BamPipe_p.cpp rename to src/api/internal/io/BamPipe_p.cpp index e13ad7c..40f1e10 100644 --- a/src/api/internal/BamPipe_p.cpp +++ b/src/api/internal/io/BamPipe_p.cpp @@ -2,12 +2,12 @@ // BamPipe_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides BAM pipe-specific IO behavior // *************************************************************************** -#include "api/internal/BamPipe_p.h" +#include "api/internal/io/BamPipe_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BamPipe_p.h b/src/api/internal/io/BamPipe_p.h similarity index 93% rename from src/api/internal/BamPipe_p.h rename to src/api/internal/io/BamPipe_p.h index 8996766..8e4e4c4 100644 --- a/src/api/internal/BamPipe_p.h +++ b/src/api/internal/io/BamPipe_p.h @@ -2,7 +2,7 @@ // BamPipe_p.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides BAM pipe-specific IO behavior // *************************************************************************** @@ -20,7 +20,7 @@ // // We mean it. -#include "api/internal/ILocalIODevice_p.h" +#include "api/internal/io/ILocalIODevice_p.h" #include namespace BamTools { diff --git a/src/api/internal/BgzfStream_p.cpp b/src/api/internal/io/BgzfStream_p.cpp similarity index 98% rename from src/api/internal/BgzfStream_p.cpp rename to src/api/internal/io/BgzfStream_p.cpp index 5891067..8b1aff6 100644 --- a/src/api/internal/BgzfStream_p.cpp +++ b/src/api/internal/io/BgzfStream_p.cpp @@ -2,7 +2,7 @@ // BgzfStream_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 11 October 2011(DB) +// Last modified: 25 October 2011(DB) // --------------------------------------------------------------------------- // Based on BGZF routines developed at the Broad Institute. // Provides the basic functionality for reading & writing BGZF files @@ -11,9 +11,9 @@ #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" +#include "api/internal/io/BamDeviceFactory_p.h" +#include "api/internal/io/BgzfStream_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/io/BgzfStream_p.h similarity index 100% rename from src/api/internal/BgzfStream_p.h rename to src/api/internal/io/BgzfStream_p.h diff --git a/src/api/internal/ILocalIODevice_p.cpp b/src/api/internal/io/ILocalIODevice_p.cpp similarity index 95% rename from src/api/internal/ILocalIODevice_p.cpp rename to src/api/internal/io/ILocalIODevice_p.cpp index 8730a91..63a3bee 100644 --- a/src/api/internal/ILocalIODevice_p.cpp +++ b/src/api/internal/io/ILocalIODevice_p.cpp @@ -2,12 +2,12 @@ // ILocalIODevice_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides shared behavior for files & pipes // *************************************************************************** -#include "api/internal/ILocalIODevice_p.h" +#include "api/internal/io/ILocalIODevice_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/ILocalIODevice_p.h b/src/api/internal/io/ILocalIODevice_p.h similarity index 100% rename from src/api/internal/ILocalIODevice_p.h rename to src/api/internal/io/ILocalIODevice_p.h diff --git a/src/api/internal/IRemoteIODevice_p.cpp b/src/api/internal/io/IRemoteIODevice_p.cpp similarity index 100% rename from src/api/internal/IRemoteIODevice_p.cpp rename to src/api/internal/io/IRemoteIODevice_p.cpp diff --git a/src/api/internal/IRemoteIODevice_p.h b/src/api/internal/io/IRemoteIODevice_p.h similarity index 100% rename from src/api/internal/IRemoteIODevice_p.h rename to src/api/internal/io/IRemoteIODevice_p.h diff --git a/src/api/internal/SamFormatParser_p.cpp b/src/api/internal/sam/SamFormatParser_p.cpp similarity index 98% rename from src/api/internal/SamFormatParser_p.cpp rename to src/api/internal/sam/SamFormatParser_p.cpp index 195fdcd..74c1fed 100644 --- a/src/api/internal/SamFormatParser_p.cpp +++ b/src/api/internal/sam/SamFormatParser_p.cpp @@ -2,15 +2,15 @@ // SamFormatParser.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides functionality for parsing SAM header text into SamHeader object // *************************************************************************** #include "api/SamConstants.h" #include "api/SamHeader.h" -#include "api/internal/BamException_p.h" -#include "api/internal/SamFormatParser_p.h" +#include "api/internal/sam/SamFormatParser_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/SamFormatParser_p.h b/src/api/internal/sam/SamFormatParser_p.h similarity index 100% rename from src/api/internal/SamFormatParser_p.h rename to src/api/internal/sam/SamFormatParser_p.h diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/sam/SamFormatPrinter_p.cpp similarity index 98% rename from src/api/internal/SamFormatPrinter_p.cpp rename to src/api/internal/sam/SamFormatPrinter_p.cpp index f9a118e..5a51a2f 100644 --- a/src/api/internal/SamFormatPrinter_p.cpp +++ b/src/api/internal/sam/SamFormatPrinter_p.cpp @@ -2,14 +2,14 @@ // SamFormatPrinter.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 14 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides functionality for printing formatted SAM header to string // *************************************************************************** #include "api/SamConstants.h" #include "api/SamHeader.h" -#include "api/internal/SamFormatPrinter_p.h" +#include "api/internal/sam/SamFormatPrinter_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/SamFormatPrinter_p.h b/src/api/internal/sam/SamFormatPrinter_p.h similarity index 100% rename from src/api/internal/SamFormatPrinter_p.h rename to src/api/internal/sam/SamFormatPrinter_p.h diff --git a/src/api/internal/SamHeaderValidator_p.cpp b/src/api/internal/sam/SamHeaderValidator_p.cpp similarity index 99% rename from src/api/internal/SamHeaderValidator_p.cpp rename to src/api/internal/sam/SamHeaderValidator_p.cpp index c76fff9..6bcb8a9 100644 --- a/src/api/internal/SamHeaderValidator_p.cpp +++ b/src/api/internal/sam/SamHeaderValidator_p.cpp @@ -2,15 +2,15 @@ // SamHeaderValidator.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 14 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides functionality for validating SamHeader data // *************************************************************************** #include "api/SamConstants.h" #include "api/SamHeader.h" -#include "api/internal/SamHeaderValidator_p.h" -#include "api/internal/SamHeaderVersion_p.h" +#include "api/internal/sam/SamHeaderValidator_p.h" +#include "api/internal/sam/SamHeaderVersion_p.h" using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/internal/SamHeaderValidator_p.h b/src/api/internal/sam/SamHeaderValidator_p.h similarity index 100% rename from src/api/internal/SamHeaderValidator_p.h rename to src/api/internal/sam/SamHeaderValidator_p.h diff --git a/src/api/internal/SamHeaderVersion_p.h b/src/api/internal/sam/SamHeaderVersion_p.h similarity index 100% rename from src/api/internal/SamHeaderVersion_p.h rename to src/api/internal/sam/SamHeaderVersion_p.h diff --git a/src/api/internal/BamException_p.cpp b/src/api/internal/utils/BamException_p.cpp similarity index 87% rename from src/api/internal/BamException_p.cpp rename to src/api/internal/utils/BamException_p.cpp index 38469e7..103e34b 100644 --- a/src/api/internal/BamException_p.cpp +++ b/src/api/internal/utils/BamException_p.cpp @@ -2,12 +2,12 @@ // BamException_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 October 2011 (DB) +// Last modified: 25 October 2011 (DB) // --------------------------------------------------------------------------- // Provides a basic exception class for BamTools internals // *************************************************************************** -#include "api/internal/BamException_p.h" +#include "api/internal/utils/BamException_p.h" using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/internal/BamException_p.h b/src/api/internal/utils/BamException_p.h similarity index 100% rename from src/api/internal/BamException_p.h rename to src/api/internal/utils/BamException_p.h -- 2.39.5