New upstream version 5.3.3+dfsg

[submodule "pbbam"]

	path = pbbam

	url = ../pbbam.git

	branch = master

[submodule "googletest"]

	path = googletest

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

	branch = master

language: cpp

script: 

  - ./travis.sh

compiler:

  - gcc

# - clang

install:

- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi

addons:

  apt:

    sources:

    - ubuntu-toolchain-r-test

    packages:

    - gcc-4.8

    - g++-4.8

#   - clang

#   - libhdf5-serial-1.8.4

notifications:

  email: false

sudo: false

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

# 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.

```

// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.

//

// All rights reserved.

//

// Redistribution and use in source and binary forms, with or without

// modification, are permitted (subject to the limitations in the

// disclaimer below) provided that the following conditions are met:

//

//  * Redistributions of source code must retain the above copyright

//    notice, this list of conditions and the following disclaimer.

//

//  * Redistributions in binary form must reproduce the above

//    copyright notice, this list of conditions and the following

//    disclaimer in the documentation and/or other materials provided

//    with the distribution.

//

//  * Neither the name of Pacific Biosciences nor the names of its

//    contributors may be used to endorse or promote products derived

//    from this software without specific prior written permission.

//

// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE

// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC

// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED

// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES

// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS

// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF

// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND

// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT

// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF

// SUCH DAMAGE.

Copyright (c) 2014-2018, Pacific Biosciences of California, Inc.

All rights reserved.

Redistribution and use in source and binary forms, with or without

modification, are permitted (subject to the limitations in the

disclaimer below) provided that the following conditions are met:

 * Redistributions of source code must retain the above copyright

   notice, this list of conditions and the following disclaimer.

 * Redistributions in binary form must reproduce the above

   copyright notice, this list of conditions and the following

   disclaimer in the documentation and/or other materials provided

   with the distribution.

 * Neither the name of Pacific Biosciences nor the names of its

   contributors may be used to endorse or promote products derived

   from this software without specific prior written permission.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE

GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC

BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED

WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES

OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS

CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF

USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND

ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT

OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF

SUCH DAMAGE.

See pbdata/MD5Utils.* for the following:

 /*

   distributed, the copyright notice must be retained and any alterations in

   the code must be clearly marked. No warranty is given regarding the quality

   of this software.*/

```