New upstream version 5.3.1+dfsg

BasedOnStyle:  Google

BreakBeforeBraces: Mozilla

AllowShortLoopsOnASingleLine: false

AccessModifierOffset: -4

BreakConstructorInitializersBeforeComma: true

ColumnLimit: 100

IndentWidth: 4

PointerAlignment: Left

TabWidth: 4

ReflowComments: false  # protect ASCII art in comments

KeepEmptyLinesAtTheStartOfBlocks: true

defines.mk

all.xml

*.h5

libconfig.h

LibBlasrConfig.h

/hdf/hdf5-1.8.12-headers/

/build

# Meson WrapDB stuff

subprojects/packagecache/

subprojects/googletest*

subprojects/pbbam*

[submodule "pbbam"]

	path = pbbam

	url = ../pbbam.git

	branch = master

[submodule "googletest"]

	path = googletest

	url = https://github.com/google/googletest.git

	branch = master

##############################################

# CMake build script for the BLASRLIBCPP library

##############################################

cmake_policy(SET CMP0048 NEW)

project(BLASRLIBCPP VERSION 5.3.0 LANGUAGES CXX C)

cmake_minimum_required(VERSION 3.6)

set(ROOT_PROJECT_NAME ${PROJECT_NAME} CACHE STRING "root project name")

# Build type

IF(NOT CMAKE_BUILD_TYPE)

    SET(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: Debug Release Profile RelWithDebInfo ReleaseWithAssert" FORCE)

ENDIF(NOT CMAKE_BUILD_TYPE)

# Main project paths

set(BLASRLIBCPP_RootDir ${BLASRLIBCPP_SOURCE_DIR})

# Project configuration

set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake ${CMAKE_MODULE_PATH})

# Fixed order, do not sort or shuffle

include(blasrlibcpp-ccache)

include(blasrlibcpp-releasewithassert)

include(blasrlibcpp-dependencies)

include(blasrlibcpp-compilerflags)

include(blasrlibcpp-gitsha1)

file(WRITE pbdata/LibBlasrConfig.h "")

GET_PROPERTY(BLASRLIBCPP_COMPIPLE_FLAGS GLOBAL PROPERTY BLASRLIBCPP_COMPIPLE_FLAGS_GLOBAL)

GET_PROPERTY(BLASRLIBCPP_LINK_FLAGS GLOBAL PROPERTY BLASRLIBCPP_LINK_FLAGS_GLOBAL)

GET_PROPERTY(HDF5_LINKER_FLAG_LOCAL GLOBAL PROPERTY HDF5_LINKER_FLAG_GLOBAL)

set(LOCAL_LINKER_FLAGS "${HDF5_LINKER_FLAG_LOCAL} ${BLASRLIBCPP_LINK_FLAGS}")

# libcpp library

file(GLOB HDF5_CPP "${BLASRLIBCPP_RootDir}/hdf/*.cpp")

file(GLOB_RECURSE ALIGNMENT_CPP "${BLASRLIBCPP_RootDir}/alignment/*.cpp")

file(GLOB_RECURSE PBDATA_CPP "${BLASRLIBCPP_RootDir}/pbdata/*.cpp")

add_library(libcpp

    ${HDF5_CPP}

    ${ALIGNMENT_CPP}

    ${PBDATA_CPP}

)

target_include_directories(libcpp PUBLIC

    ${BLASRLIBCPP_RootDir}/hdf

    ${BLASRLIBCPP_RootDir}/alignment

    ${BLASRLIBCPP_RootDir}/pbdata

    ${HDF5_INCLUDE_DIRS}

    ${PacBioBAM_INCLUDE_DIRS}

)

target_link_libraries(libcpp ${PacBioBAM_LIBRARIES})

set_target_properties(libcpp PROPERTIES COMPILE_FLAGS ${BLASRLIBCPP_COMPIPLE_FLAGS})

if (LOCAL_LINKER_FLAGS)

    set_target_properties(libcpp PROPERTIES LINK_FLAGS ${LOCAL_LINKER_FLAGS})

endif()

# Tests

enable_testing()

## build gtest

add_subdirectory(${BLASRLIBCPP_RootDir}/googletest/googletest external/gtest)

## build libcpp tests

file(GLOB_RECURSE TEST_CPP "${BLASRLIBCPP_RootDir}/unittest/*/*.cpp")

add_executable(libcpptest ${TEST_CPP})

target_include_directories(libcpptest PUBLIC ${BLASRLIBCPP_RootDir}/unittest)

target_link_libraries(libcpptest gtest_main libcpp hdf5 hdf5_cpp ${ZLIB_LDFLAGS})

add_test(libcpptest libcpptest)

set_target_properties(libcpptest PROPERTIES COMPILE_FLAGS "${BLASRLIBCPP_COMPIPLE_FLAGS}")

if (LOCAL_LINKER_FLAGS)

    set_target_properties(libcpptest PROPERTIES LINK_FLAGS ${LOCAL_LINKER_FLAGS})

endif()

add_custom_target(check_libcpp

    COMMAND libcpptest --gtest_output=xml:${CMAKE_BINARY_DIR}/libcpp-unit.xml

    WORKING_DIRECTORY ${BLASRLIBCPP_RootDir})

# Developer environment

## Clang-format pre commit hook

### What?

The intention here is to get source code formatting automatically

checked and guaranteed before checkin.

### Why?

- Automate style-guide compliance to avoid squabbles

- Post-checkin reformatting binges mess up history.  It's best to get

  it right from the get-go.

### How?

See the tools:

  - `tools/check-formatting --staged` for fast style-checking of

    changed files, in a git commit/push hook;

  - `tools/check-formatting --all` for slower style-checking of everything

  - `tools/format-all`to format everything

To enable the checking as a pre-commit hook, place the following in

`.git/hooks/pre-commit` (and make that file executable):

```sh

#!/bin/bash

./tools/check-formatting --staged

```

### Tips

- We should *not* reformat bundled third-party code as it will make it

  difficult to diff with upstream.  Put such code in a subdirectory

  with its own .clang-format file containing: "BasedOnStyle: None" to

  disable formatting.

- If clang-format mangles something (for example, a comment block with

  ASCII art or significant whitespace), you can protect a block using

  `// clang-format off` and then `// clang-format on`.

* What are these binaries?

  The `clang-format` binaries that are checked in are static builds of

  clang-format v3.9 from https://github.com/angular/clang-format.

  They are bundled because the LLVM toolchain has a reputation for

  rapid change and incompatibility.  We want to guarantee that devs

  are using the same version as CI is.