[med-svn] [bamtools] 06/10: Refresh patches
Andreas Tille
tille at debian.org
Fri Jan 13 14:45:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bamtools.
commit bf3bf5bef8c0569c2e7996c1582a10f3d111eb2b
Author: Andreas Tille <tille at debian.org>
Date: Fri Jan 13 10:31:18 2017 +0100
Refresh patches
---
.../patches/0002-support-out-of-source-build.patch | 14 +++------
.../0006-Fix-Doxyfile-input-source-path.patch | 30 ------------------
debian/patches/0007-Big_Endian.patch | 12 +++-----
debian/patches/0008_Cmake_Test.patch | 8 ++---
debian/patches/doxygen-tweak | 36 +++-------------------
debian/patches/gcc-6_compat | 20 ------------
debian/patches/series | 2 --
debian/patches/spelling | 17 ++--------
8 files changed, 20 insertions(+), 119 deletions(-)
diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch
index ae8f236..d93d2d3 100644
--- a/debian/patches/0002-support-out-of-source-build.patch
+++ b/debian/patches/0002-support-out-of-source-build.patch
@@ -8,12 +8,10 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/117
src/toolkit/CMakeLists.txt | 2 +-
3 files changed, 5 insertions(+), 4 deletions(-)
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index dade1e3..c4f5ab7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 4 )
- set( BamTools_VERSION_BUILD 0 )
+ set( BamTools_VERSION_BUILD 1 )
# set our library and executable destination dirs
-set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
@@ -23,7 +21,7 @@ index dade1e3..c4f5ab7 100644
# define compiler flags for all code
set( CMAKE_BUILD_TYPE Release )
-@@ -60,6 +60,7 @@ endif()
+@@ -61,6 +61,7 @@ endif()
# add our includes root path
include_directories( src )
@@ -31,11 +29,9 @@ index dade1e3..c4f5ab7 100644
# list subdirectories to build in
add_subdirectory( src )
-diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake
-index ec62573..ddfe410 100644
--- a/src/ExportHeader.cmake
+++ b/src/ExportHeader.cmake
-@@ -18,7 +18,7 @@ function( ExportHeader MODULE FILE DEST )
+@@ -18,7 +18,7 @@ function( ExportHeader MODULE FILE DEST
add_custom_command( TARGET ${MODULE} COMMAND
${CMAKE_COMMAND} -E copy_if_different
"${CMAKE_CURRENT_SOURCE_DIR}/${FILE}"
@@ -44,11 +40,9 @@ index ec62573..ddfe410 100644
# make sure files are properly 'installed'
install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" )
-diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
-index d074870..e6a2da9 100644
--- a/src/toolkit/CMakeLists.txt
+++ b/src/toolkit/CMakeLists.txt
-@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROPERTIES
+@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROP
OUTPUT_NAME "bamtools"
)
# make version info available in application
diff --git a/debian/patches/0006-Fix-Doxyfile-input-source-path.patch b/debian/patches/0006-Fix-Doxyfile-input-source-path.patch
deleted file mode 100644
index 43ebfbd..0000000
--- a/debian/patches/0006-Fix-Doxyfile-input-source-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From: Kevin Murray <spam at kdmurray.id.au>
-Date: Thu, 24 Sep 2015 18:04:10 +1000
-Subject: Fix Doxyfile input source path
-Forwarded: https://github.com/pezmaster31/bamtools/pull/118
----
- docs/Doxyfile | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/docs/Doxyfile b/docs/Doxyfile
-index 2a0f578..5632082 100644
---- a/docs/Doxyfile
-+++ b/docs/Doxyfile
-@@ -590,7 +590,7 @@ WARN_LOGFILE =
- # directories like "/usr/src/myproject". Separate the files or directories
- # with spaces.
-
--INPUT = /home/derek/development/bamtools/src/api
-+INPUT = src/api
-
- # This tag can be used to specify the character encoding of the source files
- # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-@@ -649,7 +649,7 @@ RECURSIVE = YES
- # excluded from the INPUT source files. This way you can easily exclude a
- # subdirectory from a directory tree whose root is specified with the INPUT tag.
-
--EXCLUDE = /home/derek/development/bamtools/src/api/internal
-+EXCLUDE = src/api/internal
-
- # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
- # directories that are symbolic links (a Unix filesystem feature) are excluded
diff --git a/debian/patches/0007-Big_Endian.patch b/debian/patches/0007-Big_Endian.patch
index efc75ad..2a329ac 100644
--- a/debian/patches/0007-Big_Endian.patch
+++ b/debian/patches/0007-Big_Endian.patch
@@ -3,13 +3,11 @@ Author: Dominique Belhachemi <domibel at debian.org>
Bug-Debian: https://bugs.debian.org/807979
Forwarded: https://github.com/pezmaster31/bamtools/pull/119
-Index: bamtools/src/api/BamAux.h
-===================================================================
---- bamtools.orig/src/api/BamAux.h
-+++ bamtools/src/api/BamAux.h
-@@ -424,8 +424,15 @@ API_EXPORT inline unsigned int UnpackUns
- API_EXPORT inline unsigned short UnpackUnsignedShort(const char* buffer) {
- union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;
+--- a/src/api/BamAux.h
++++ b/src/api/BamAux.h
+@@ -370,8 +370,15 @@ API_EXPORT inline signed int UnpackSigne
+ API_EXPORT inline signed short UnpackSignedShort(const char* buffer) {
+ union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;
un.value = 0;
+#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
un.valueBuffer[0] = buffer[0];
diff --git a/debian/patches/0008_Cmake_Test.patch b/debian/patches/0008_Cmake_Test.patch
index 5499768..fe542f1 100644
--- a/debian/patches/0008_Cmake_Test.patch
+++ b/debian/patches/0008_Cmake_Test.patch
@@ -2,10 +2,8 @@ Description: run simple test after compilation
The test suite can be extended once we add some small and simple bam files.
Author: Dominique Belhachemi <domibel at debian.org>
-Index: bamtools/CMakeLists.txt
-===================================================================
---- bamtools.orig/CMakeLists.txt
-+++ bamtools/CMakeLists.txt
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
@@ -8,6 +8,8 @@
# set project name
project( BamTools )
@@ -15,7 +13,7 @@ Index: bamtools/CMakeLists.txt
# Cmake requirements
cmake_minimum_required( VERSION 2.6.4 )
-@@ -64,3 +66,11 @@ include_directories("${CMAKE_BINARY_DIR}
+@@ -65,3 +67,11 @@ include_directories("${CMAKE_BINARY_DIR}
# list subdirectories to build in
add_subdirectory( src )
diff --git a/debian/patches/doxygen-tweak b/debian/patches/doxygen-tweak
index 400ab28..452a144 100644
--- a/debian/patches/doxygen-tweak
+++ b/debian/patches/doxygen-tweak
@@ -2,35 +2,9 @@ From: Michael R. Crusoe <crusoe at ucdavis.edu>
Subject: fixes a couple Doxygen warnings
Forwarded: https://github.com/pezmaster31/bamtools/pull/120
---- bamtools.orig/src/api/BamMultiReader.cpp
-+++ bamtools/src/api/BamMultiReader.cpp
-@@ -361,10 +361,10 @@
- method can be useful when you know, for example, that your BAM files are sorted
- by coordinate but upstream processes did not set the header tag properly.
-
-- \note This method should \bold not be called while reading alignments via
-+ \note This method should \b not be called while reading alignments via
- GetNextAlignment() or GetNextAlignmentCore(). For proper results, you should
- call this method before (or immediately after) opening files, rewinding,
-- jumping, etc. but \bold not once alignment fetching has started. There is
-+ jumping, etc. but \b not once alignment fetching has started. There is
- nothing in the API to prevent you from doing so, but the results may be
- unexpected.
-
---- bamtools.orig/docs/Doxyfile
-+++ bamtools/docs/Doxyfile
-@@ -1454,7 +1454,7 @@
- # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
- # containing the font.
-
--DOT_FONTNAME = FreeSans
-+# DOT_FONTNAME = FreeSans
-
- # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
- # The default size is 10pt.
---- bamtools.orig/src/api/BamAlignment.h
-+++ bamtools/src/api/BamAlignment.h
-@@ -143,12 +143,13 @@
+--- a/src/api/BamAlignment.h
++++ b/src/api/BamAlignment.h
+@@ -143,12 +143,13 @@ class API_EXPORT BamAlignment {
bool SkipToNextTag(const char storageType,
char*& pTagData,
unsigned int& numBytesParsed) const;
@@ -46,7 +20,7 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/120
// data members
std::string AllCharData;
uint32_t BlockLength;
-@@ -156,7 +157,8 @@
+@@ -156,7 +157,8 @@ class API_EXPORT BamAlignment {
uint32_t QueryNameLength;
uint32_t QuerySequenceLength;
bool HasCoreOnly;
@@ -56,7 +30,7 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/120
// constructor
BamAlignmentSupportData(void)
: BlockLength(0)
-@@ -171,7 +173,6 @@
+@@ -171,7 +173,6 @@ class API_EXPORT BamAlignment {
friend class Internal::BamWriterPrivate;
mutable std::string ErrorString; // mutable to allow updates even in logically const methods
diff --git a/debian/patches/gcc-6_compat b/debian/patches/gcc-6_compat
deleted file mode 100644
index f1a168d..0000000
--- a/debian/patches/gcc-6_compat
+++ /dev/null
@@ -1,20 +0,0 @@
-From d5c951f45ed768570df65e29ba9ab9eef2369f37 Mon Sep 17 00:00:00 2001
-From: Matei David <matei at cs.toronto.edu>
-Date: Wed, 3 Feb 2016 23:50:26 -0500
-Subject: [PATCH] add c++98 compile and link flag
-Forwarded: https://github.com/pezmaster31/bamtools/pull/116
-
----
- CMakeLists.txt | 1 +
- 1 file changed, 1 insertion(+)
-
---- bamtools.orig/CMakeLists.txt
-+++ bamtools/CMakeLists.txt
-@@ -42,6 +42,7 @@
-
- # define compiler flags for all code
- set( CMAKE_BUILD_TYPE Release )
-+set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" )
- add_definitions( -Wall -D_FILE_OFFSET_BITS=64 )
-
- # -----------------------------------------------
diff --git a/debian/patches/series b/debian/patches/series
index d399e0c..ea86059 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,8 +5,6 @@ non-deprecated-jsoncpp-function-names
0003-remove-custom-ExportHeader-function-use-install-inst.patch
0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
0006-Doxygen-reproducibility
-0006-Fix-Doxyfile-input-source-path.patch
0007-Big_Endian.patch
0008_Cmake_Test.patch
spelling
-gcc-6_compat
diff --git a/debian/patches/spelling b/debian/patches/spelling
index a34dd09..d3a0ae8 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -2,20 +2,9 @@ From: Michael R. Crusoe <crusoe at ucdavis.edu>
Subject: Fix typo
Forwarded: https://github.com/pezmaster31/bamtools/pull/122
---- bamtools.orig/src/toolkit/bamtools_split.cpp
-+++ bamtools/src/toolkit/bamtools_split.cpp
-@@ -199,7 +199,7 @@
-
- // if we get here, no property was specified
- cerr << "bamtools split ERROR: no property given to split on... " << endl
-- << "Please use -mapped, -paired, -reference, or -tag TAG to specifiy desired split behavior." << endl;
-+ << "Please use -mapped, -paired, -reference, or -tag TAG to specify desired split behavior." << endl;
- return false;
- }
-
---- bamtools.orig/src/toolkit/bamtools_resolve.cpp
-+++ bamtools/src/toolkit/bamtools_resolve.cpp
-@@ -868,7 +868,7 @@
+--- a/src/toolkit/bamtools_resolve.cpp
++++ b/src/toolkit/bamtools_resolve.cpp
+@@ -868,7 +868,7 @@ bool ResolveTool::ResolveToolPrivate::Ch
// make sure required stats file supplied
if ( !m_settings->HasStatsFile )
--
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