cmake/FindHTSlib.cmake

+# Find HTSlib
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(HTSlib REQUIRED htslib)
+
+# because CMake is trying to be extra clever,
+# it will not properly load libraries with
+# absolute paths in *_LIBRARIES
+set(HTSlib_LIBRARIES "${HTSlib_LDFLAGS}")
+
+message(STATUS "   HTSlib include dirs: ${HTSlib_INCLUDE_DIRS}")
+message(STATUS "   HTSlib libraries: ${HTSlib_LIBRARIES}")

cmake/PbbamTool.cmake

+include(CMakeParseArguments)
+
+function(create_pbbam_tool)
+
+    # parse args
+    set(oneValueArgs TARGET)
+    set(multiValueArgs SOURCES)
+    cmake_parse_arguments(create_pbbam_tool "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    # create executable
+    include_directories(
+        ${ToolsCommonDir}           # shared tool code
+        ${GeneratedDir}             # generated version headers
+        ${PacBioBAM_INCLUDE_DIRS}   # pbbam/htslib includes
+    )
+    add_executable(${create_pbbam_tool_TARGET} ${create_pbbam_tool_SOURCES})
+    set_target_properties(
+        ${create_pbbam_tool_TARGET} PROPERTIES
+        RUNTIME_OUTPUT_DIRECTORY ${PacBioBAM_BinDir}
+    )
+    target_link_libraries(${create_pbbam_tool_TARGET} pbbam)
+
+endfunction(create_pbbam_tool)

cmake/pbbam-ccache.cmake

+
+if(PacBioBAM_use_ccache)
+    find_program(CCACHE_FOUND ccache)
+    if(CCACHE_FOUND)
+        set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
+        set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK    ccache)
+    endif()
+endif()

cmake/pbbam-compilerflags.cmake

+
+include(CheckCXXCompilerFlag)
+
+# C++11 check & enabling
+if (CMAKE_VERSION VERSION_LESS "3.1")
+    if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")    # clang
+    else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")        # gcc
+    endif()
+else() # 3.1+
+    set(CMAKE_CXX_STANDARD          14)
+    set(CMAKE_CXX_STANDARD_REQUIRED ON)
+endif()
+
+# shared CXX flags for src & tests
+if (MSVC)
+    set(PacBioBAM_CXX_FLAGS "/Wall")
+else()
+    set(PacBioBAM_CXX_FLAGS "-Wall")
+endif()
+
+# NOTE: -Wno-unused-local-typedefs used to quash clang warnings w/ Boost
+check_cxx_compiler_flag("-Wno-unused-local-typedefs" HAS_NO_UNUSED_LOCAL_TYPEDEFS)
+if(HAS_NO_UNUSED_LOCAL_TYPEDEFS)
+    set(PacBioBAM_CXX_FLAGS "${PacBioBAM_CXX_FLAGS} -Wno-unused-local-typedefs")
+endif()
+
+check_cxx_compiler_flag("-Wno-sign-compare" HAS_NO_SIGN_COMPARE)
+if(HAS_NO_SIGN_COMPARE)
+    set(PacBioBAM_CXX_FLAGS "${PacBioBAM_CXX_FLAGS} -Wno-sign-compare")
+endif()
+
+# Turn on windows-style filepath resolution.
+# We need to add this #define early (not just in the C# SWIG wrapper)
+if(WIN32)
+    add_definitions(-DPBBAM_WIN_FILEPATHS)
+endif()
+
+# For now, keep @rpath out of install names on OS X, as it causes SWIG
+# tests to fail.
+if(APPLE)
+    set(CMAKE_MACOSX_RPATH OFF)
+endif()

cmake/pbbam-dependencies.cmake

+
+# pthreads
+find_package(Threads REQUIRED)
+
+# boost
+if(NOT Boost_INCLUDE_DIRS)
+    find_package(Boost REQUIRED)
+endif()
+
+# Winsock for htslib on Windows
+if(WIN32)
+    set(SOCKET_LIBRARIES "ws2_32")
+endif()
+
+# zlib
+if (NOT ZLIB_INCLUDE_DIRS OR NOT ZLIB_LIBRARIES)
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(ZLIB zlib)
+    set(ZLIB_LIBRARIES ${ZLIB_LDFLAGS})
+else()
+    set(ZLIB_LDFLAGS ${ZLIB_LIBRARIES})
+endif()
+
+# htslib
+if(NOT HTSLIB_INCLUDE_DIRS OR NOT HTSLIB_LIBRARIES)
+    find_package(HTSlib)
+    set(hts_INCLUDE_DIRS ${HTSlib_INCLUDE_DIRS})
+    set(hts_LIBRARIES    ${HTSlib_LIBRARIES})
+else()    
+    set(hts_INCLUDE_DIRS ${HTSLIB_INCLUDE_DIRS})
+    set(hts_LIBRARIES    ${HTSLIB_LIBRARIES})
+endif()

cmake/pbbam-libtype.cmake

+
+# determine if we need a shared lib
+if(PacBioBAM_build_shared)
+    set(BUILD_SHARED_LIBS ON)
+    set(htslib_build_shared ON CACHE BOOL "force htslibConfig to export proper library name")
+    set(PB_LIB_MODE SHARED)
+    set(PB_LIB_SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX})
+else()
+    set(BUILD_SHARED_LIBS OFF)
+    set(PB_LIB_MODE STATIC)
+    set(PB_LIB_SUFFIX ${CMAKE_STATIC_LIBRARY_SUFFIX})
+endif()
+
+if(WIN32)
+    # Limit the number of DLLs we will have to bundle
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+  set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+endif()
+
+
+

debian/changelog

@@ -9,6 +9,7 @@ pbbam (0.18.0+dfsg-1) UNRELEASED; urgency=medium
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.2.1
   * Use d-shlibs
+  * Remove unneeded trigger
 
   [ Fabian Kloetzl ]
   * fix dependency check for meson

debian/control

@@ -27,7 +27,7 @@ Package: pbbamtools
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libpbbam (= ${binary:Version})
+         libpbbam0.18.0 (= ${binary:Version})
 Recommends: samtools
 Description: processing Pacific Biosciences binary alignment/map files
  The BAM format is a binary, compressed, record-oriented container format

debian/copyright

@@ -3,6 +3,7 @@ Upstream-Name: pbbam
 Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
 Source: https://github.com/PacificBiosciences/pbbam
 Files-Excluded: third-party
+                */clang-format*
 
 Files: *
 Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>

debian/libpbbam0.18.0.triggers

-activate-noawait	ldconfig