.clang-format

+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

.gitignore

@@ -76,3 +76,7 @@ CMakeLists.txt.user
 bin
 build
 lib
+
+# Meson WrapDB stuff
+subprojects/packagecache/
+subprojects/googletest*

CHANGELOG.md

@@ -3,9 +3,25 @@
 ## Active
 
 ### TODO
-- Interface groups
 - Initial sequence-related data structures
 
+## [0.3.0] - 2018-04-30
+
+### Changed
+- Minor ToolContract::Config API change.
+
+## [0.2.0] - 2017-12-03
+
+### Added
+- WorkQueue for parallel execution
+
+## [0.1.1] - 2017-09-26
+
+### Changed
+- UNUSED macro to no-op method
+
+## [0.1.0] - 2017-01-13
+
 ### Added
 - Encapsulate project version and git sha1
 - RSMovieName & RSReadName: Sequel and RSII movie names are composed of
@@ -13,6 +29,10 @@ different data, and thus need to be handled separately. MovieName & ReadName
 handle Sequel-style data as the default.
 - GoogleTest/GoogleMock in third-party/googletest
 - Access to input command line from PacBio::CLI::Results
+- QGramIndex & seed results
+- Added support for new tool contract data model: option choices & modified JSON
+format.
+- Added basic option groups to CLI::Interface.
 
 ## [0.0.1] - 2016-06-22
 
@@ -29,21 +49,21 @@ handle Sequel-style data as the default.
   - MovieName - query parts of a PacBio movie name
   - ReadName - query parts of a PacBio read name
 - **PacBio::JSON** : JSON support
-  - Json - wrapper around nlohmann::json 
+  - Json - wrapper around nlohmann::json
 - **PacBio::Logging** : logging utilities
   - Logger, LogMessage, etc - basic logging (same as pbccs)
 - **PacBio::Stream** : functional-programming-like data streaming
   - data Source, Sink, & Transform typedefs
   - instantiated with client-defined 'callables' (lambdas, free functions,
   static public member functions)
-  - connected via operator >> 
+  - connected via operator >>
 - **PacBio::Utility** : miscellaneous utilities
   - CallbackTimer - schedule periodic callback invokation (or delayed
   single-shot)
   - EnumClassHash - allows enums/enum classes to be used as STL hash keys
   - Stopwatch - timer for benchmarking, logging, etc
   - StringUtils - string dicing & splicing utilities
-  - SystemInfo - currently provides endianness 
+  - SystemInfo - currently provides endianness
 - Examples
   - cli_demo - playground for testing the command line interface
 - Tests

CMakeLists.txt

@@ -2,9 +2,9 @@
 # CMake build script for PacBio pbcopper library.
 ########################################################################
 cmake_policy(SET CMP0048 NEW)  # lets us set version in project()
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.2)
 
-project(pbcopper VERSION 0.0.1 LANGUAGES CXX C)
+project(pbcopper VERSION 0.4.0 LANGUAGES CXX C)
 enable_testing()
 
 # project options
@@ -40,8 +40,12 @@ include(pbcopper-libtype)
 include(pbcopper-gitsha1)
 find_git_sha1(COPPER_GIT_SHA1)
 configure_file(
-    ${pbcopper_IncludeDir}/pbcopper/utility/Version.h.in
-    ${CMAKE_BINARY_DIR}/generated/pbcopper/utility/Version.h
+    ${pbcopper_SourceDir}/utility/PbcopperGitHash.cpp.in
+    ${CMAKE_BINARY_DIR}/generated/utility/PbcopperGitHash.cpp
+)
+configure_file(
+    ${pbcopper_SourceDir}/utility/PbcopperVersion.cpp.in
+    ${CMAKE_BINARY_DIR}/generated/utility/PbcopperVersion.cpp
 )
 
 # main library

LICENSE.txt

-Copyright (c) 2016, Pacific Biosciences of California, Inc.
+Copyright (c) 2016-2018, Pacific Biosciences of California, Inc.
 
 All rights reserved.
 

README.md

 # pbcopper [![CircleCI](https://circleci.com/gh/PacificBiosciences/pbcopper.svg?style=svg&circle-token=4fe4468113a44b8b76019c901f1b6930ef26944b)](https://circleci.com/gh/PacificBiosciences/pbcopper)
 
-The **pbcopper** library provides a suite of data structures, algorithms, and utilities 
-for C++ applications. 
+The **pbcopper** library provides a suite of data structures, algorithms, and utilities
+for C++ applications.
 
 ## Getting Started
 
@@ -13,7 +13,7 @@ mkdir build && cd build
 cmake ..
 make
 ```
- 
+
 To build & run tests:
 
 ```sh
@@ -32,7 +32,7 @@ To build Doxygen API documentation: (**not yet available**)
 make docs
 ```
 
-## API Overview - main modules 
+## API Overview - main modules
 
 - **PacBio::CLI** : command-line parsing & tool-contract integration
   - CLI - entry-point methods for parsing args & invoking application callback
@@ -44,19 +44,19 @@ make docs
   - MovieName - query parts of a PacBio movie name
   - ReadName - query parts of a PacBio read name
 - **PacBio::JSON** : JSON support
-  - Json - wrapper around [nlohmann::json](https://github.com/nlohmann/json) 
+  - Json - wrapper around [nlohmann::json](https://github.com/nlohmann/json)
 - **PacBio::Logging** : logging utilities
   - Logger, LogMessage, etc - basic logging (same as pbccs)
 - **PacBio::Stream** : functional-programming-like data streaming
   - data Source, Sink, & Transform typedefs
   - instantiated with client-defined 'callables' (lambdas, free functions, static public member functions)
-  - connected via operator >> 
+  - connected via operator >>
 - **PacBio::Utility** : miscellaneous utilities
   - CallbackTimer - schedule periodic callback invokation (or delayed single-shot)
   - EnumClassHash - allows enums/enum classes to be used as STL hash keys
   - Stopwatch - timer for benchmarking, logging, etc
   - StringUtils - string dicing & splicing utilities
-  - SystemInfo - currently provides endianness 
+  - SystemInfo - currently provides endianness
 
 ##  Documentation
 
@@ -66,3 +66,7 @@ make docs
 ## License
 
  - [PacBio open source license](https://github.com/PacificBiosciences/pbcopper/blob/master/LICENSE.txt)
+
+DISCLAIMER
+----------
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

bamboo_build.sh

+#!/usr/bin/env bash
+set -vex
+
+################
+# DEPENDENCIES #
+################
+
+## Load modules
+type module >& /dev/null || . /mnt/software/Modules/current/init/bash
+
+module purge
+
+module load meson
+module load ninja
+
+module load boost
+module load doxygen
+
+
+BOOST_ROOT="${BOOST_ROOT%/include}"
+# unset these variables to have meson discover all
+# boost-dependent variables from BOOST_ROOT alone
+unset BOOST_INCLUDEDIR
+unset BOOST_LIBRARYDIR
+
+export CC="ccache gcc"
+export CXX="ccache g++"
+export CCACHE_BASEDIR="${PWD}"
+
+if [[ $USER == bamboo ]]; then
+  export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.${bamboo_shortPlanKey}.ccachedir
+  export CCACHE_TEMPDIR=/scratch/bamboo.ccache_tempdir
+fi
+
+case "${bamboo_planRepository_branchName}" in
+  develop|master)
+    export PREFIX_ARG="/mnt/software/p/pbcopper/${bamboo_planRepository_branchName}"
+    export BUILD_NUMBER="${bamboo_globalBuildNumber:-0}"
+    ;;
+  *)
+    export BUILD_NUMBER="0"
+    ;;
+esac
+
+# in order to make shared libraries consumable
+# by conda and other package managers
+export LDFLAGS="-static-libstdc++ -static-libgcc"
+
+for i in "system-gcc" "gcc/8.1.0" "gcc"; do
+  # 1. load either current MOBS GCC or RHEL-default GCC
+  if [[ ${i} == system-gcc ]]; then
+    module load gtest/gcc48
+  else
+    module load ${i} gtest
+  fi
+  module load ccache
+
+  export CURRENT_BUILD_DIR="build_gcc=${i/\//_}"
+  export ENABLED_TESTS="true"
+
+  bash scripts/ci/build.sh
+  bash scripts/ci/test.sh
+
+  module unload ccache gtest
+  [[ ${i} != system-gcc ]] && module unload gcc
+done
+
+# create symlink so Bamboo can find the xunit output
+ln -s "${CURRENT_BUILD_DIR}" build
+
+if [[ -z ${PREFIX_ARG+x} ]]; then
+  echo "Not installing anything (branch: ${bamboo_planRepository_branchName}), exiting."
+  exit 0
+fi
+
+# reload GCC to prevent default `g++` from mis-linking
+module load gcc
+
+bash scripts/ci/install.sh
+
+if [[ ${BUILD_NUMBER} == 0 ]]; then
+  echo "Build number is 0, hence not creating artifact"
+  exit 0
+fi
+
+## Creating artifact
+# install into staging dir with --prefix /usr/local
+# in order to sidestep all the artifact policy
+rm -rf staging
+meson configure -Dprefix=/usr/local -Dtests=false "${CURRENT_BUILD_DIR}"
+DESTDIR="${PWD}/staging" ninja -C "${CURRENT_BUILD_DIR}" -v install
+
+( cd staging && tar zcf ../pbcopper-SNAPSHOT.tgz . )
+md5sum  pbcopper-SNAPSHOT.tgz | awk -e '{print $1}' >| pbcopper-SNAPSHOT.tgz.md5
+sha1sum pbcopper-SNAPSHOT.tgz | awk -e '{print $1}' >| pbcopper-SNAPSHOT.tgz.sha1
+
+UNSUPPORTED_URL=http://ossnexus.pacificbiosciences.com/repository/unsupported
+curl -vn --upload-file pbcopper-SNAPSHOT.tgz      $UNSUPPORTED_URL/gcc-6.4.0/pbcopper-SNAPSHOT.tgz
+curl -vn --upload-file pbcopper-SNAPSHOT.tgz.md5  $UNSUPPORTED_URL/gcc-6.4.0/pbcopper-SNAPSHOT.tgz.md5
+curl -vn --upload-file pbcopper-SNAPSHOT.tgz.sha1 $UNSUPPORTED_URL/gcc-6.4.0/pbcopper-SNAPSHOT.tgz.sha1

bamboo_coverage.sh

+#!/usr/bin/env bash
+set -vex
+
+## Load modules
+type module >& /dev/null || . /mnt/software/Modules/current/init/bash
+
+module purge
+
+module load gcc
+module load ccache
+
+module load meson
+module load ninja
+
+module load boost
+module load doxygen
+module load gcov
+module load gtest
+
+#####################
+# BUILD & RUN TESTS #
+#####################
+
+rm -rf build
+mkdir build 
+cd build
+
+meson \
+  --werror \
+  --backend ninja \
+  --buildtype debug \
+  --default-library shared \
+  --libdir lib \
+  --wrap-mode nofallback \
+  --prefix "${PREFIX_ARG:-/usr/local}" \
+  -Db_coverage=true \
+  ..
+
+ninja test
+
+############
+# COVERAGE #
+############
+
+find . -type f -iname '*.o' | xargs gcov -acbrfu {} \; >/dev/null && \
+mkdir coverage && pushd coverage && mv ../*.gcov . && \
+sed -i -e 's@Source:@Source:../@' *.gcov && \
+sed -i -e 's@Graph:@Graph:../@' *.gcov && \
+sed -i -e 's@Data:@Data:../@' *.gcov 

bamboo_test.sh

+#!/usr/bin/env bash
+
+echo "################"
+echo "# DEPENDENCIES #"
+echo "################"
+
+echo "## Load modules"
+source /mnt/software/Modules/current/init/bash
+
+module load gcc meson ccache ninja gtest
+if [[ $USER == "bamboo" ]]; then
+  export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir
+  export CCACHE_TEMPDIR=/scratch/bamboo.ccache_tempdir
+fi
+export CCACHE_COMPILERCHECK='%compiler% -dumpversion'
+export CCACHE_BASEDIR=$PWD
+
+
+echo "#########"
+echo "# TESTS #"
+echo "#########"
+
+echo "## Unit tests"
+ninja -C build test

build.sh

@@ -3,7 +3,8 @@
 echo "# DEPENDENCIES"
 echo "## Load modules"
 source /mnt/software/Modules/current/init/bash
-module load gcc/5.3.0 cmake ccache ninja boost doxygen
+module load gcc cmake ccache ninja boost doxygen
+export CC=gcc CXX=g++
 
 echo "# BUILD"
 echo "## Create build directory "
@@ -18,4 +19,4 @@ echo "## Build source"
 
 echo "# TEST"
 echo "# Run unit tests"
-( cd build &&  ninja check-xunit )
\ No newline at end of file
+( cd build &&  ninja check-xunit )

circle.yml

 
 machine:
-  pre: 
+  pre:
     - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 20
     - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 20
 

cmake/pbcopper-compilerflags.cmake

 
 include(CheckCXXCompilerFlag)
 
-# shared CXX flags for all source code & tests
-if (MSVC)
-    set(pbcopper_CXX_FLAGS "/Wall")
-else()
-    set(pbcopper_CXX_FLAGS "-std=c++11 -Wall")
-endif()
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
 
 # NOTE: quash clang warnings w/ Boost
 check_cxx_compiler_flag("-Wno-unused-local-typedefs" HAS_NO_UNUSED_LOCAL_TYPEDEFS)

docs/meson.build

+error('pbcopper doesn\'t support Doxygen yet')

examples/cli_demo/main.cpp

@@ -4,17 +4,16 @@
 #include <string>
 using namespace PacBio;
 using namespace PacBio::CLI;
-using namespace std;
 
 struct MyAppSettings {
     bool progress;
     bool force;
     bool verbose;
-    string tempDir;
+    std::string tempDir;
     int timeout;
-    string source;
-    string dest;
-    vector<string> extras;
+    std::string source;
+    std::string dest;
+    std::vector<std::string> extras;
 };
 
 static inline
@@ -23,20 +22,20 @@ int RunMain(const MyAppSettings& s)
     // this is where your normal app would take its settings and start rocking
     // here, we just print out what we received from the CL
 
-    cout << "--------------------" << endl
-         << "App Settings:       " << endl
-         << "--------------------" << endl
-         << "progress?  " << (s.progress ? "on" : "off") << endl
-         << "force?     " << (s.force ? "on" : "off") << endl
-         << "verbose?   " << (s.verbose ? "on" : "off") << endl
-         << "tempDir:   " << s.tempDir << endl
-         << "timeout:   " << s.timeout << endl
-         << "source:    " << s.source << endl
-         << "dest:      " << s.dest << endl
+    std::cout << "--------------------\n"
+         << "App Settings:       \n"
+         << "--------------------\n"
+         << "progress?  " << (s.progress ? "on" : "off") << '\n'
+         << "force?     " << (s.force ? "on" : "off") << '\n'
+         << "verbose?   " << (s.verbose ? "on" : "off") << '\n'
+         << "tempDir:   " << s.tempDir << '\n'
+         << "timeout:   " << s.timeout << '\n'
+         << "source:    " << s.source << '\n'
+         << "dest:      " << s.dest << '\n'
          << "extras:    ";
     for (const auto& extra : s.extras )
-        cout << extra << ", ";
-    cout << endl;
+        std::cout << extra << ", ";
+    std::cout << '\n';
 
     return EXIT_SUCCESS;
 }
@@ -85,7 +84,7 @@ int argRunner(const PacBio::CLI::Results& args)
 
     const auto positionalArgs = args.PositionalArguments();
     if (positionalArgs.size() < 2) {
-        cerr << "ERROR: source & dest args are required" << endl;
+        std::cerr << "ERROR: source & dest args are required\n";
         PacBio::CLI::PrintHelp(args.ApplicationInterface(), std::cout);
         return EXIT_FAILURE;
     }

examples/cli_demo/meson.build

+executable(
+  'cli_demo',
+  files('main.cpp'),
+  install : false,
+  include_directories : pbcopper_include_directories,
+  link_with : pbcopper_lib,
+  dependencies : pbcopper_thread_dep)

examples/meson.build

+subdir('cli_demo')

include/meson.build

+###########
+# headers #
+###########
+
+if not meson.is_subproject()
+
+  # pbcopper
+  install_headers(
+    files([
+      'pbcopper/PbcopperConfig.h',
+      'pbcopper/PbcopperMakeUnique.h']),
+    subdir : 'pbcopper')
+
+  # pbcopper/align
+  install_headers(
+    files([
+      'pbcopper/align/Seed.h',
+      'pbcopper/align/Seeds.h']),
+    subdir : 'pbcopper/align')
+
+  # pbcopper/align/internal
+  install_headers(
+    files([
+      'pbcopper/align/internal/Seed-inl.h',
+      'pbcopper/align/internal/Seeds-inl.h']),
+    subdir : 'pbcopper/align/internal')
+
+  # pbcopper/cli
+  install_headers(
+    files([
+      'pbcopper/cli/CLI.h',
+      'pbcopper/cli/HelpPrinter.h',
+      'pbcopper/cli/Interface.h',
+      'pbcopper/cli/Option.h',
+      'pbcopper/cli/OptionFlags.h',
+      'pbcopper/cli/Parser.h',
+      'pbcopper/cli/PositionalArg.h',
+      'pbcopper/cli/Results.h',
+      'pbcopper/cli/SingleDashMode.h',
+      'pbcopper/cli/VersionPrinter.h']),
+    subdir : 'pbcopper/cli')
+
+  # pbcopper/cli/internal
+  install_headers(
+    files([
+      'pbcopper/cli/internal/Option-inl.h']),
+    subdir : 'pbcopper/cli/internal')
+
+  # pbcopper/cli/toolcontract
+  install_headers(
+    files([
+      'pbcopper/cli/toolcontract/Config.h',
+      'pbcopper/cli/toolcontract/Driver.h',
+      'pbcopper/cli/toolcontract/InputFileType.h',
+      'pbcopper/cli/toolcontract/JsonPrinter.h',
+      'pbcopper/cli/toolcontract/OutputFileType.h',
+      'pbcopper/cli/toolcontract/ResolvedToolContract.h',
+      'pbcopper/cli/toolcontract/ResourceType.h',
+      'pbcopper/cli/toolcontract/Task.h',
+      'pbcopper/cli/toolcontract/TaskType.h']),
+    subdir : 'pbcopper/cli/toolcontract')
+
+  # pbcopper/cli/toolcontract/internal
+  install_headers(
+    files([
+      'pbcopper/cli/toolcontract/internal/Driver-inl.h',
+      'pbcopper/cli/toolcontract/internal/InputFileType-inl.h',
+      'pbcopper/cli/toolcontract/internal/OutputFileType-inl.h',
+      'pbcopper/cli/toolcontract/internal/Task-inl.h']),
+    subdir : 'pbcopper/cli/toolcontract/internal')
+
+  # pbcopper/data
+  install_headers(
+    files([
+      'pbcopper/data/CCSTag.h',
+      'pbcopper/data/Cigar.h',
+      'pbcopper/data/CigarOperation.h',
+      'pbcopper/data/Interval.h',
+      'pbcopper/data/MovieName.h',
+      'pbcopper/data/Position.h',
+      'pbcopper/data/ReadName.h',
+      'pbcopper/data/RSMovieName.h',
+      'pbcopper/data/RSReadName.h',
+      'pbcopper/data/Zmw.h']),
+    subdir : 'pbcopper/data')
+
+  # pbcopper/data/internal
+  install_headers(
+    files([
+      'pbcopper/data/internal/CigarOperation-inl.h',
+      'pbcopper/data/internal/Interval-inl.h',
+      'pbcopper/data/internal/MovieName-inl.h',
+      'pbcopper/data/internal/ReadNameBase-inl.h',
+      'pbcopper/data/internal/ReadNameBase.h',
+      'pbcopper/data/internal/RSMovieName-inl.h']),
+    subdir : 'pbcopper/data/internal')
+
+  # pbcopper/json
+  install_headers(
+    files([
+      'pbcopper/json/JSON.h']),
+    subdir : 'pbcopper/json')
+
+  # pbcopper/json/internal
+  install_headers(
+    files([
+      'pbcopper/json/internal/json.hpp']),
+    subdir : 'pbcopper/json/internal')
+
+  # pbcopper/logging
+  install_headers(
+    files([
+      'pbcopper/logging/Logging.h']),
+    subdir : 'pbcopper/logging')
+
+  # pbcopper/logging/internal
+  install_headers(
+    files([
+      'pbcopper/logging/internal/Logging-inl.h']),
+    subdir : 'pbcopper/logging/internal')
+
+  # pbcopper/parallel
+  install_headers(
+    files([
+      'pbcopper/parallel/FireAndForget.h',
+      'pbcopper/parallel/WorkQueue.h']),
+    subdir : 'pbcopper/parallel')
+
+  # pbcopper/qgram
+  install_headers(
+    files([
+      'pbcopper/qgram/Index.h',
+      'pbcopper/qgram/IndexHit.h',
+      'pbcopper/qgram/IndexHits.h']),
+    subdir : 'pbcopper/qgram')
+
+  # pbcopper/qgram/internal
+  install_headers(
+    files([
+      'pbcopper/qgram/internal/Hashing-inl.h',
+      'pbcopper/qgram/internal/Index-inl.h']),
+    subdir : 'pbcopper/qgram/internal')
+
+  # pbcopper/stream
+  install_headers(
+    files([
+      'pbcopper/stream/Stream.h']),
+    subdir : 'pbcopper/stream')
+
+  # pbcopper/utility
+  install_headers(
+    files([
+      'pbcopper/utility/CallbackTimer.h',
+      'pbcopper/utility/EnumClassHash.h',
+      'pbcopper/utility/FileUtils.h',
+      'pbcopper/utility/MoveAppend.h',
+      'pbcopper/utility/PbcopperVersion.h',
+      'pbcopper/utility/SafeSubtract.h',
+      'pbcopper/utility/Stopwatch.h',
+      'pbcopper/utility/StringUtils.h',
+      'pbcopper/utility/SystemInfo.h',
+      'pbcopper/utility/Unused.h']),
+    subdir : 'pbcopper/utility')
+
+  # pbcopper/utility/internal
+  install_headers(
+    files([
+      'pbcopper/utility/internal/CallbackTimer-inl.h',
+      'pbcopper/utility/internal/FileUtils-inl.h',
+      'pbcopper/utility/internal/Stopwatch-inl.h',
+      'pbcopper/utility/internal/StringUtils-inl.h',
+      'pbcopper/utility/internal/SystemInfo-inl.h']),
+    subdir : 'pbcopper/utility/internal')
+endif
+
+pbcopper_include_directories = include_directories('.')

include/pbcopper/Config.h

-#ifndef PBCOPPER_CONFIG_H
-#define PBCOPPER_CONFIG_H
-
-#include <cstddef>
-#include <cstdint>
-
-#define UNUSED(x) (void)x
-
-namespace PacBio {
-
-///// \internal
-//enum class Initialization
-//{
-//    Uninitialized
-//};
-
-///// \internal
-//static constexpr Initialization Uninitialized = Initialization::Uninitialized;
-
-} // namespace PacBio
-
-#endif // PBCOPPER_CONFIG_H

include/pbcopper/PbcopperConfig.h

+// Author: David Seifert, Derek Barnett
+
+// Reduce the number of exposed symbols in order to speed up
+// DSO load times
+// https://gcc.gnu.org/wiki/Visibility
+
+#ifndef PBCOPPER_PBCOPPERCONFIG_H
+#define PBCOPPER_PBCOPPERCONFIG_H
+
+// clang-format off
+#if defined _WIN32 || defined __CYGWIN__
+#  ifdef PBCOPPER_BUILDING_LIBRARY
+#    ifdef __GNUC__
+#      define PBCOPPER_PUBLIC_API __attribute__((dllexport))
+#    else
+#      define PBCOPPER_PUBLIC_API __declspec(dllexport)  // Note: gcc seems to also supports this syntax
+#    endif
+#  else
+#    ifdef __GNUC__
+#      define PBCOPPER_PUBLIC_API __attribute__((dllimport))
+#    else
+#      define PBCOPPER_PUBLIC_API __declspec(dllimport)  // Note: gcc seems to also supports this syntax
+#    endif
+#  endif
+#  define PBCOPPER_PRIVATE_API
+#else
+#  if __GNUC__ >= 4
+#    define PBCOPPER_PUBLIC_API __attribute__((visibility("default")))
+#    define PBCOPPER_PRIVATE_API __attribute__((visibility("hidden")))
+#  else
+#    define PBCOPPER_PUBLIC_API
+#    define PBCOPPER_PRIVATE_API
+#  endif
+#endif
+// clang-format on
+
+#endif  // PBCOPPER_PBCOPPERCONFIG_H

include/pbcopper/PbcopperMakeUnique.h

+// File Description
+//
+// Author: Derek Barnett, David Seifert
+
+// Yes, this include guard needs to be called
+// "PBBAM_MAKE_UNIQUE_H", in order to prevent
+// clashes with the same wrapper in pbbam
+#ifndef PBBAM_MAKE_UNIQUE_H
+#define PBBAM_MAKE_UNIQUE_H
+
+// Only include if in pre-C++14 mode
+//
+#if __cplusplus < 201402L
+
+#include <cstddef>
+#include <memory>
+
+namespace std {
+
+template <typename T, typename... Args>
+inline std::unique_ptr<T> make_unique(Args&&... args)
+{
+    return std::unique_ptr<T>(new T(std::forward<Args>(args)...));
+}
+
+}  // namespace std
+
+#endif  // < C++14
+
+#endif  // PBBAM_MAKE_UNIQUE_H