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commit 0a9961e543848ec7a9c0635fd2580982bf26ad7c Author: Dominique Belhachemi <[email protected]> Date: Sun Dec 20 17:29:28 2015 -0500 allow to read bam files on big endian systems --- debian/changelog | 7 +++++++ debian/copyright | 1 + debian/patches/0007-Big_Endian.patch | 25 +++++++++++++++++++++++++ debian/patches/0008_Cmake_Test.patch | 25 +++++++++++++++++++++++++ debian/patches/series | 2 ++ 5 files changed, 60 insertions(+) diff --git a/debian/changelog b/debian/changelog index 0a92d7c..0a77457 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +bamtools (2.4.0+dfsg-3) unstable; urgency=medium + + * allow to read bam files on big endian systems (Closes: #807979) + * activated cmake testing framework, tests need to be added + + -- Dominique Belhachemi <[email protected]> Sun, 20 Dec 2015 15:41:42 -0500 + bamtools (2.4.0+dfsg-2) unstable; urgency=medium [ Kevin Murray ] diff --git a/debian/copyright b/debian/copyright index 4a89112..d7ac49c 100644 --- a/debian/copyright +++ b/debian/copyright @@ -14,6 +14,7 @@ Files: debian/* Copyright: 2012 Michael R. Crusoe <[email protected]> 2014 Andreas Tille <[email protected]> 2015 Kevin Murray <[email protected]> + 2012,2015 Dominique Belhachemi <[email protected]> License: Expat License: Expat diff --git a/debian/patches/0007-Big_Endian.patch b/debian/patches/0007-Big_Endian.patch new file mode 100644 index 0000000..e9235d4 --- /dev/null +++ b/debian/patches/0007-Big_Endian.patch @@ -0,0 +1,25 @@ +Description: read bam files on big endian systems +Author: Dominique Belhachemi <[email protected]> +Bug-Debian: https://bugs.debian.org/807979 +Forwarded: https://github.com/pezmaster31/bamtools/issues/113 + +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; + un.value = 0; ++#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__ + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; ++#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ ++ un.valueBuffer[0] = buffer[1]; ++ un.valueBuffer[1] = buffer[0]; ++#else ++ #error "Unsupported hardware" ++#endif + return un.value; + } + diff --git a/debian/patches/0008_Cmake_Test.patch b/debian/patches/0008_Cmake_Test.patch new file mode 100644 index 0000000..35ac9cf --- /dev/null +++ b/debian/patches/0008_Cmake_Test.patch @@ -0,0 +1,25 @@ +Description: run simple test after compilation + The test suite can be extended once we add some small and simple bam files. +Author: Dominique Belhachemi <[email protected]> + +Index: bamtools/CMakeLists.txt +=================================================================== +--- bamtools.orig/CMakeLists.txt ++++ bamtools/CMakeLists.txt +@@ -8,6 +8,8 @@ + # set project name + project( BamTools ) + ++enable_testing() ++ + # Cmake requirements + cmake_minimum_required( VERSION 2.6.4 ) + +@@ -64,3 +66,7 @@ include_directories("${CMAKE_BINARY_DIR} + + # list subdirectories to build in + add_subdirectory( src ) ++ ++add_test(NAME bamtools ++ COMMAND bin/bamtools --help ++) diff --git a/debian/patches/series b/debian/patches/series index 0f5a38c..8e3563c 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -4,3 +4,5 @@ 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bamtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
