.gitignore

+# This file is used to ignore files which are generated
+# ----------------------------------------------------------------------------
+
+*~
+*.autosave
+*.a
+*.core
+*.moc
 *.o
-*.pico
+*.obj
+*.orig
+*.rej
 *.so
-*.a
-*.dylib
-*.pyc
-*~
+*.so.*
+*_pch.h.cpp
+*_resource.rc
+*.qm
+.#*
+*.*#
+core
+!core/
+tags
+.DS_Store
+.directory
+*.debug
+Makefile*
+*.prl
+*.app
+moc_*.cpp
+ui_*.h
+qrc_*.cpp
+Thumbs.db
+*.res
+*.rc
+/.qmake.cache
+/.qmake.stash
+
+# qtcreator generated files
+*.pro.user*
 CMakeLists.txt.user
-bin/
-build/
-docs/Doxyfile
-lib/
-tests/bin/test_pbbam
-tests/data/test_group_query/group.fofn
-tests/src/TestData.h
+
+# xemacs temporary files
+*.flc
+
+# Vim temporary files
+.*.swp
+
+# Visual Studio generated files
+*.ib_pdb_index
+*.idb
+*.ilk
+*.pdb
+*.sln
+*.suo
+*.vcproj
+*vcproj.*.*.user
+*.ncb
+*.sdf
+*.opensdf
+*.vcxproj
+*vcxproj.*
+
+.vscode
+
+# MinGW generated files
+*.Debug
+*.Release
+
+# Python byte code
+*.pyc
+
+# Binaries
+# --------
+*.dll
+*.exe
+
+# Generated directories
+bin
+build
+lib
 
 # Meson WrapDB stuff
 subprojects/packagecache/
 subprojects/googletest*
+
+# generated Doxyfile
+*Doxyfile

CHANGELOG.md

@@ -10,6 +10,39 @@ guarantees will be maintained within each major version series.
 
 ## Active
 
+## [0.23.0] - 2019-03-11
+
+### Added
+ - PbiIndexCache and FastaCache for reusing file data
+ - BaiIndexedBamReader and GenomicIntervalQuery can be constructed without
+   initial interval.
+
+## [0.22.0] - 2019-02-11
+
+### Fixed
+ - Handles zero-length reads for stitching ZMW reads.
+ - Clipping to query on reverse-strand aligned reads.
+ - Removed UB in dataset API.
+
+### Added
+ - "exciseFlankingInserts" option for clipping reads w.r.t reference.
+
+## [0.21.0] - 2018-12-21
+
+### Added
+ - New local context flags: ADAPTER_BEFORE_BAD and ADAPTER_AFTER_BAD.
+
+### Changed
+ - Current PacBioBAM spec now 3.0.7.
+
+### Removed
+ - CMake has been removed completely.
+
+## [0.20.0] - 2018-10-03
+
+### Added
+ - Support for (optionally) barcode-labeled read group IDs.
+
 ## [0.19.0] - 2018-09-11
 
 ### Added

CMakeLists.txt

-########################################################################
-# CMake build script for PacBioBAM library.
-########################################################################
-
-cmake_policy(SET CMP0048 NEW)  # lets us set version in project()
-project(PacBioBAM VERSION 0.19.0 LANGUAGES CXX C)
-cmake_minimum_required(VERSION 3.0)
-
-# project name & version
-set(PacBioBAM_NAME pbbam)
-set(PacBioBAM_VERSION
-  "${PacBioBAM_VERSION_MAJOR}.${PacBioBAM_VERSION_MINOR}.${PacBioBAM_VERSION_PATCH}"
-)
-
-# list build-time options
-option(PacBioBAM_build_docs    "Build PacBioBAM's API documentation."                   ON)
-option(PacBioBAM_build_tests   "Build PacBioBAM's unit tests."                          ON)
-option(PacBioBAM_build_shared  "Build PacBioBAM as shared library as well."             OFF)
-option(PacBioBAM_build_tools   "Build PacBioBAM command line utilities (e.g. pbindex)"  ON)
-option(PacBioBAM_use_modbuild  "Build PacBioBAM using Modular Build System."            OFF)
-option(PacBioBAM_use_ccache    "Build PacBioBAM using ccache, if available."            ON)
-option(PacBioBAM_auto_validate "Build PacBioBAM with auto-validation enabled."          OFF)
-
-if(PacBioBAM_build_tests)
-    enable_testing()
-endif()
-
-set(PacBioBAM_permissive_cigar  OFF)
-STRING(TOLOWER "${PBBAM_PERMISSIVE_CIGAR}" PBBAM_PERMISSIVE_CIGAR_LOWER)
-if (DEFINED PBBAM_PERMISSIVE_CIGAR)
-    set(PacBioBAM_permissive_cigar  ON)
-    add_definitions(-DPBBAM_PERMISSIVE_CIGAR)
-endif()
-
-# project paths
-set(PacBioBAM_RootDir       ${CMAKE_CURRENT_LIST_DIR})
-set(PacBioBAM_DocsDir       ${PacBioBAM_RootDir}/docs)
-set(PacBioBAM_IncludeDir    ${PacBioBAM_RootDir}/include)
-set(PacBioBAM_SourceDir     ${PacBioBAM_RootDir}/src)
-set(PacBioBAM_TestsDir      ${PacBioBAM_RootDir}/tests)
-set(PacBioBAM_ThirdPartyDir ${PacBioBAM_RootDir}/third-party)
-set(PacBioBAM_ToolsDir      ${PacBioBAM_RootDir}/tools)
-
-if(NOT PacBioBAM_OutputDir)
-    set(PacBioBAM_OutputDir ${CMAKE_CURRENT_BINARY_DIR})
-endif()
-set(PacBioBAM_BinDir    ${PacBioBAM_OutputDir}/bin)
-set(PacBioBAM_LibDir    ${PacBioBAM_OutputDir}/lib)
-
-set(GeneratedDir ${CMAKE_BINARY_DIR}/generated)
-set(GeneratedTestDataDir ${GeneratedDir}/data)
-file(MAKE_DIRECTORY ${PacBioBAM_BinDir})
-file(MAKE_DIRECTORY ${PacBioBAM_LibDir})
-file(MAKE_DIRECTORY ${GeneratedDir})
-file(MAKE_DIRECTORY ${GeneratedTestDataDir})
-
-# project configuration (keep this order)
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake ${CMAKE_MODULE_PATH})
-include(pbbam-ccache)
-include(pbbam-compilerflags)
-include(pbbam-libtype)
-include(pbbam-dependencies)
-
-# project components (keep this order)
-add_subdirectory(src)
-add_subdirectory(tools)
-add_subdirectory(docs)
-add_subdirectory(tests)

bamboo_build.sh

@@ -22,104 +22,33 @@ module load boost
 module load cram
 
 
-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
-
+export BUILD_NUMBER="0"
 case "${bamboo_planRepository_branchName}" in
   develop|master)
+    _install_image_default="${INSTALL_IMAGE:-false}"
+    _create_artifact_default="${CREATE_ARTIFACT:-false}"
+
     export PREFIX_ARG="/mnt/software/p/pbbam/${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"
-
-# i : unity build
-for i in "on" "off"; do
-  for j in "system-gcc" "gcc/8.1.0" "gcc"; do
-    # 1. load either current MOBS GCC or RHEL-default GCC
-    if [[ ${j} == system-gcc ]]; then
-      module load gtest/gcc48
-    else
-      module load ${j} gtest
-    fi
-    module load ccache
+export _install_image="${_install_image_default:-false}"
+export _create_artifact="${_create_artifact_default:-false}"
 
-    export CURRENT_BUILD_DIR="build_unity=${i^^}_gcc=${j/\//_}"
-    export ENABLED_TESTS="true"
-    export ENABLED_UNITY_BUILD="${i}"
 
-    bash scripts/ci/build.sh
-    bash scripts/ci/test.sh
-
-    module unload ccache gtest
-    [[ ${j} != system-gcc ]] && module unload gcc
-  done
-done
-
-# create symlink so Bamboo can find the xunit output
-ln -s "${CURRENT_BUILD_DIR}" build
-
-if [[ -z ${PREFIX_ARG+x} ]]; then
-  echo "Not installing anything (branch: ${bamboo_planRepository_branchName}), exiting."
-  exit 0
-fi
-
-bash scripts/ci/install.sh
-
-if [[ ${BUILD_NUMBER} == 0 ]]; then
-  echo "Build number is 0, hence not creating artifact"
-  exit 0
-fi
-
-echo "## Creating artifact"
-# install into staging dir with --prefix /usr/local
-# in order to sidestep all the artifact policy
-rm -rf staging
-meson configure -Dprefix=/usr/local -Dtests=false "${CURRENT_BUILD_DIR}"
-DESTDIR="${PWD}/staging" ninja -C "${CURRENT_BUILD_DIR}" -v install
-
-if [[ ${BUILD_NUMBER} = 0 ]]; then
-  exit 0
-elif [[ $bamboo_planRepository_branchName == master ]]; then
-  VERSION="$(${CURRENT_BUILD_DIR}/tools/bam2sam --version)".${BUILD_NUMBER}
-  NEXUS_REPO=maven-releases
-elif [[ $bamboo_planRepository_branchName == develop ]]; then
-  VERSION="$(${CURRENT_BUILD_DIR}/tools/bam2sam --version)".SNAPSHOT${BUILD_NUMBER}
-  NEXUS_REPO=maven-snapshots
-  rm -rf /mnt/secondary/builds/unsupported/pbbam.previous
-  if [[ -e /mnt/secondary/builds/unsupported/pbbam ]]; then
-    mv /mnt/secondary/builds/unsupported/pbbam \
-       /mnt/secondary/builds/unsupported/pbbam.previous
-  fi
-  DESTDIR="/mnt/secondary/builds/unsupported/pbbam/" ninja -C "${CURRENT_BUILD_DIR}" -v install
-else
-  exit 0
-fi
-NEXUS_VERSION="$(${CURRENT_BUILD_DIR}/tools/bam2sam --version)".${BUILD_NUMBER}
+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
 
-( cd staging && tar zcf ../pbbam-${VERSION}-x86_64.tgz . )
-md5sum  pbbam-${VERSION}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${VERSION}-x86_64.tgz.md5
-sha1sum pbbam-${VERSION}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${VERSION}-x86_64.tgz.sha1
+# in order to make shared libraries consumable
+# by conda and other package managers
+export LDFLAGS="-static-libstdc++ -static-libgcc"
 
-NEXUS_URL=http://ossnexus.pacificbiosciences.com/repository/${NEXUS_REPO}/pacbio/sat/pbbam/pbbam/${NEXUS_VERSION}
-curl -vn --upload-file pbbam-${VERSION}-x86_64.tgz      ${NEXUS_URL}/gcc-6.4.0/pbbam-${VERSION}-x86_64.tgz
-curl -vn --upload-file pbbam-${VERSION}-x86_64.tgz.md5  ${NEXUS_URL}/gcc-6.4.0/pbbam-${VERSION}-x86_64.tgz.md5
-curl -vn --upload-file pbbam-${VERSION}-x86_64.tgz.sha1 ${NEXUS_URL}/gcc-6.4.0/pbbam-${VERSION}-x86_64.tgz.sha1
+source scripts/ci/setup.sh
+source scripts/ci/build.sh
+source scripts/ci/test.sh
+source scripts/ci/install.sh
+source scripts/ci/artifact.sh

bamboo_build_itg.sh

-#!/bin/bash -vex
-type module >& /dev/null || . /mnt/software/Modules/current/init/bash
-
-module load cmake
-module load ccache
-export CCACHE_DIR="/mnt/secondary/Share/tmp/bamboo.${bamboo_shortPlanKey}.ccache"
-
-HTSLIB_VERSION=$(/bin/ls -d src/htslib-*|sed -e 's/.*htslib-//'|sort -V|tail -1)
-PBBAM_VERSION=$(grep 'PacBioBAM VERSION ' src/pbbam/CMakeLists.txt|sed -e 's/.*VERSION //'|awk '{print $1}')
-# project(PacBioBAM VERSION 0.14.0 LANGUAGES CXX C)
-BUILD_NUMBER=0
-if [ -n "$bamboo_planRepository_branchName" ]; then
-  BUILD_NUMBER=${bamboo_globalBuildNumber:-0}
-fi
-
-rm -f *.tgz || true
-rm -rf pbbam* || true
-rm -rf prefix && mkdir -p prefix
-PREFIX=$(readlink -f prefix)
-cd src/htslib-${HTSLIB_VERSION}
-export CCACHE_BASEDIR=$PWD
-make distclean
-CC=gcc CFLAGS='-fPIC -O' bash ./configure --prefix=$PWD/../../prefix --disable-bz2 --disable-lzma --disable-libcurl
-VERBOSE=1 make install
-rm -rf $PWD/../../prefix/lib/pkgconfig
-
-cd -
-cd src/pbbam
-export CCACHE_BASEDIR=$PWD
-rm -rf build && mkdir -p build
-cd build
-curl -sL -O http://nexus/repository/maven-thirdparty/libquadmath/4.8.5-11/libquadmath-devel-4.8.5-11.el7.x86_64.rpm
-rpm2cpio libquadmath-devel-4.8.5-11.el7.x86_64.rpm | cpio -vid
-CXXFLAGS="-fPIC -I$PWD/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include" \
-CFLAGS="-fPIC" \
-cmake \
-  -DCMAKE_CXX_COMPILER="g++" \
-  -DCMAKE_C_COMPILER="gcc" \
-  -DPacBioBAM_build_shared=ON \
-  -DPacBioBAM_build_docs=OFF \
-  -DPacBioBAM_build_tests=OFF \
-  -DHTSLIB_INCLUDE_DIRS=$PREFIX/include \
-  -DHTSLIB_LIBRARIES=$PREFIX/lib/libhts.a \
-  -DBoost_INCLUDE_DIRS=/mnt/software/b/boost/1.60/include \
-  -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-  -DCMAKE_SKIP_BUILD_RPATH=FALSE ..
-VERBOSE=1 make -j
-tar c bin lib | tar xv -C ../../../prefix/
-cd ..
-tar c include/pbbam | tar xv -C ../../prefix/
-cd ../..
-
-if [ ! -n "$bamboo_planRepository_branchName" ]; then
-  SNAPSHOT="_branch_"
-fi
-if [ "$bamboo_planRepository_branchName" = "develop" ]; then
-  SNAPSHOT="SNAPSHOT"
-elif [ "$bamboo_planRepository_branchName" = "master" ]; then
-  SNAPSHOT=""
-else
-  SNAPSHOT="_branch_"
-fi
-
-rsync -ax --delete prefix/ pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}/
-
-tar zcf pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}
-sha1sum pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1
-md5sum  pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5
-
-if [ "$bamboo_planRepository_branchName" = "develop" ]; then
-  NEXUS_URL=http://ossnexus.pacificbiosciences.com/repository/maven-snapshots/pacbio/itg/pbbam/${PBBAM_VERSION}.${BUILD_NUMBER}
-elif [ "$bamboo_planRepository_branchName" = "master" ]; then
-  NEXUS_URL=http://ossnexus.pacificbiosciences.com/repository/maven-releases/pacbio/itg/pbbam/${PBBAM_VERSION}.${BUILD_NUMBER}
-else
-  echo "[INFO] pbbam-${PBBAM_VERSION}.SNAPSHOT${BUILD_NUMBER}-x86_64.tgz if the branch was develop"
-  exit
-fi
-curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5  $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5
-curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1 $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1
-curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz      $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz

bamboo_build_pa.sh

-#!/bin/bash -vex
-type module >& /dev/null || . /mnt/software/Modules/current/init/bash
-
-module use /mnt/software/modulefiles
-module use /pbi/dept/primary/modulefiles
-
-module load cmake
-module load ccache
-export CCACHE_DIR="/mnt/secondary/Share/tmp/bamboo.${bamboo_shortPlanKey}.ccache"
-# module load composer_xe/2017.4.196
-
-HTSLIB_VERSION=$(/bin/ls -d src/htslib-*|sed -e 's/.*htslib-//'|sort -V|tail -1)
-PBBAM_VERSION=$(grep 'PacBioBAM VERSION ' src/pbbam/CMakeLists.txt|sed -e 's/.*VERSION //'|awk '{print $1}')
-# project(PacBioBAM VERSION 0.14.0 LANGUAGES CXX C)
-BUILD_NUMBER=0
-if [ -n "$bamboo_planRepository_branchName" ]; then
-  BUILD_NUMBER=${bamboo_globalBuildNumber:-0}
-fi
-
-rm -f *.tgz || true
-rm -rf pbbam* || true
-# rm -rf prefix && mkdir -p prefix
-# cd src/htslib-${HTSLIB_VERSION}
-# export CCACHE_BASEDIR=$PWD
-# CC=icc CXX=icpc \
-# CFLAGS='-fPIC -Os' bash ./configure --prefix=$PWD/../../prefix
-# VERBOSE=1 make CC='ccache icc' install
-# rm -rf $PWD/../../prefix/lib/pkgconfig
-# 
-# cd -
-# cd src/pbbam
-# export CCACHE_BASEDIR=$PWD
-# rm -rf build && mkdir -p build
-# cd build
-# cmake \
-#   -DCMAKE_CXX_COMPILER="ccache" \
-#   -DCMAKE_CXX_COMPILER_ARG1="icpc -fPIC" \
-#   -DCMAKE_C_COMPILER="ccache" \
-#   -DCMAKE_C_COMPILER_ARG1="icc -fPIC" \
-#   -DPacBioBAM_build_shared=OFF \
-#   -DPacBioBAM_build_docs=OFF \
-#   -DPacBioBAM_build_tests=OFF \
-#   -DHTSLIB_INCLUDE_DIRS=$PWD/../../../prefix/include \
-#   -DHTSLIB_LIBRARIES=$PWD/../../../prefix/lib/libhts.a \
-#   -DBoost_INCLUDE_DIRS=/mnt/software/b/boost/1.60/include \
-#   -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-#   -DCMAKE_SKIP_BUILD_RPATH=FALSE ..
-# VERBOSE=1 make -j
-# tar c bin lib | tar xv -C ../../../prefix/
-# cd ..
-# tar c include/pbbam | tar xv -C ../../prefix/
-# cd ../..
-# 
-# if [ ! -n "$bamboo_planRepository_branchName" ]; then
-#   SNAPSHOT="_branch_"
-# fi
-# if [ "$bamboo_planRepository_branchName" = "develop" ]; then
-#   SNAPSHOT="SNAPSHOT"
-# elif [ "$bamboo_planRepository_branchName" = "master" ]; then
-#   SNAPSHOT=""
-# else
-#   SNAPSHOT="_branch_"
-# fi
-# 
-# rsync -ax --delete prefix/ pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}/
-# 
-# tar zcf pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}
-# sha1sum pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1
-# md5sum  pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5
-# if [ "$bamboo_planRepository_branchName" = "develop" -o "$bamboo_planRepository_branchName" = "master" ]; then
-#   NEXUS_URL=http://ossnexus.pacificbiosciences.com/repository/maven-snapshots/pacbio/seq/pa/pbbam/${PBBAM_VERSION}.${BUILD_NUMBER}
-#   curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5  $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5
-#   curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1 $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1
-#   curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz      $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz
-# else
-#   echo "[INFO] pbbam-${PBBAM_VERSION}.SNAPSHOT${BUILD_NUMBER}-x86_64.tgz if the branch is develop"
-# fi
-
-# GCC BUILD
-
-# module unload composer_xe/2017.4.196
-# module load gcc/4.9.2
-rm -rf prefix && mkdir -p prefix
-cd src/htslib-${HTSLIB_VERSION}
-export CCACHE_BASEDIR=$PWD
-make distclean
-CC=gcc CFLAGS='-fPIC -O' bash ./configure --prefix=$PWD/../../prefix --disable-bz2 --disable-lzma --disable-libcurl
-VERBOSE=1 make install
-rm -rf $PWD/../../prefix/lib/pkgconfig
-
-cd -
-cd src/pbbam
-export CCACHE_BASEDIR=$PWD
-rm -rf build && mkdir -p build
-cd build
-curl -sL -O http://nexus/repository/maven-thirdparty/libquadmath/4.8.5-11/libquadmath-devel-4.8.5-11.el7.x86_64.rpm
-rpm2cpio libquadmath-devel-4.8.5-11.el7.x86_64.rpm | cpio -vid
-CXXFLAGS="-fPIC -I$PWD/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include" \
-CFLAGS="-fPIC" \
-cmake \
-  -DCMAKE_CXX_COMPILER="g++" \
-  -DCMAKE_C_COMPILER="gcc" \
-  -DPacBioBAM_build_shared=OFF \
-  -DPacBioBAM_build_docs=OFF \
-  -DPacBioBAM_build_tests=OFF \
-  -DHTSLIB_INCLUDE_DIRS=$PWD/../../../prefix/include \
-  -DHTSLIB_LIBRARIES=$PWD/../../../prefix/lib/libhts.a \
-  -DBoost_INCLUDE_DIRS=/mnt/software/b/boost/1.60/include \
-  -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-  -DCMAKE_SKIP_BUILD_RPATH=FALSE ..
-VERBOSE=1 make -j
-tar c bin lib | tar xv -C ../../../prefix/
-cd ..
-tar c include/pbbam | tar xv -C ../../prefix/
-cd ../..
-
-if [ ! -n "$bamboo_planRepository_branchName" ]; then
-  SNAPSHOT="_branch_"
-fi
-if [ "$bamboo_planRepository_branchName" = "develop" ]; then
-  SNAPSHOT="SNAPSHOT"
-elif [ "$bamboo_planRepository_branchName" = "master" ]; then
-  SNAPSHOT=""
-else
-  SNAPSHOT="_branch_"
-fi
-
-rsync -ax --delete prefix/ pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}/
-
-tar zcf pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}
-sha1sum pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1
-md5sum  pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz | awk -e '{print $1}' >| pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5
-if [ "$bamboo_planRepository_branchName" = "develop" ]; then
-  NEXUS_URL=http://ossnexus.pacificbiosciences.com/repository/maven-snapshots/pacbio/seq/pa/pbbam/${PBBAM_VERSION}.${BUILD_NUMBER}
-elif [ "$bamboo_planRepository_branchName" = "master" ]; then
-  NEXUS_URL=http://ossnexus.pacificbiosciences.com/repository/maven-releases/pacbio/seq/pa/pbbam/${PBBAM_VERSION}.${BUILD_NUMBER}
-else
-  echo "[INFO] pbbam-${PBBAM_VERSION}.SNAPSHOT${BUILD_NUMBER}-x86_64.tgz if the branch was develop"
-  echo "[INFO] pbbam-${PBBAM_VERSION}.${BUILD_NUMBER}-x86_64.tgz if the branch was master"
-  exit
-fi
-curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5  $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.md5
-curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1 $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz.sha1
-curl -L -fvn --upload-file pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz      $NEXUS_URL/pbbam-${PBBAM_VERSION}.${SNAPSHOT}${BUILD_NUMBER}-x86_64.tgz

bamboo_coverage.sh

-#!/usr/bin/env bash
-set -xve
-
-source /mnt/software/Modules/current/init/bash
-module load gcc meson ccache ninja zlib htslib samtools cram boost gtest gcov
-
-echo "#####################"
-echo "# BUILD & RUN TESTS #"
-echo "#####################"
-
-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
-
-echo "################"
-echo "# COVERAGE     #"
-echo "################"
-
-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 && \
-rm pugixml*
-

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()
-
-
-

docs/CMakeLists.txt

-find_package(Doxygen)
-
-if(DOXYGEN_FOUND)
-    configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${PacBioBAM_DocsDir}/Doxyfile @ONLY )
-    add_custom_target(doc
-        ${DOXYGEN_EXECUTABLE} ${PacBioBAM_DocsDir}/Doxyfile
-        WORKING_DIRECTORY ${PacBioBAM_DocsDir}
-        COMMENT "Generating API documentation with Doxygen"
-        VERBATIM
-    )
-endif()

docs/source/conf.py

@@ -103,9 +103,9 @@ author = u'Derek Barnett'
 # built documents.
 #
 # The short X.Y version.
-version = '0.17.0'
+version = '0.23.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.17.0'
+release = '0.23.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/getting_started.rst

@@ -25,14 +25,10 @@ Double-check your compiler version, to be sure it is compatible.
 Additional requirements:
 
 * `Boost`_ (1.55+)
-* `CMake`_ (3.0+)
+* `Meson`_ (0.48+)
 * `Google Test`_
 * `htslib`_ (1.4+)
 
-For additional languages:
-
-* `SWIG`_ (3.0.5+)
-
 For building API documentation locally:
 
 * `Doxygen`_
@@ -41,14 +37,12 @@ For maximal convenience, install htslib and google test in the same parent direc
 
 .. _Boost: http://www.boost.org/
 .. _clang: http://clang.llvm.org/
-.. _CMake: https://cmake.org/
-.. _Meson: http://mesonbuild.com/
+.. _Meson: https://mesonbuild.com
 .. _Ninja: https://ninja-build.org/ (only required when using Meson, optional for CMake)
 .. _Doxygen: http://www.stack.nl/~dimitri/doxygen/
 .. _gcc: https://gcc.gnu.org/
 .. _Google Test: https://github.com/google/googletest
 .. _htslib: https://github.com/samtools/htslib.git 
-.. _SWIG: http://www.swig.org/
 
 .. _getting_started-build:
 
@@ -75,51 +69,6 @@ You should first clone the repository:
    $ git clone https://github.com/PacificBiosciences/pbbam.git
    $ cd pbbam
 
-Building with CMake
-^^^^^^^^^^^^^^^^^^^
-
-When building with CMake, create a separate build directory:
-
-.. code-block:: console
-
-   $ mkdir build
-   $ cd build
-   $ cmake ..
-   $ make -j 4    # compiles using 4 threads
-
-Output:
-
-  * Library   : <pbbam_root>/lib
-  * Headers   : <pbbam_root>/include
-  * Utilities : <pbbam_root>/bin
- 
-You may need to set a few options on the cmake command, to point to dependencies' install locations. 
-Common installation-related options include:
-
-  * GTEST_SRC_DIR
-  
-Add these using the '-D' argument, like this:
-
-.. code-block:: console
-
-   $ cmake .. -DGTEST_SRC_DIR="path/to/googletest"
- 
-To run the test suite, run:
-
-.. code-block:: console
-
-   $ make test
-
-To build a local copy of the (Doxygen-style) API documentation, run:
-
-.. code-block:: console
-
-   $ make doc
-   
-And then open <pbbam_root>/docs/html/index.html in your favorite browser.
-
-.. _getting_started-integrate:
-
 Building with Meson
 ^^^^^^^^^^^^^^^^^^^
 
@@ -151,42 +100,6 @@ and ninja will install pbbam to ``/my/install/prefix``.
 Integrate
 ---------
 
-CMake-based projects
-````````````````````
-
-For CMake-based projects that will "ship with" or otherwise live alongside pbbam, you can 
-use the approach described here.
-
-Before defining your library or executable, add the following:
-
-.. code-block:: cmake
-
-   add_subdirectory(<path/to/pbbam> external/build/pbbam)
-
-When it's time to run "make" this will ensure that pbbam will be built, inside your own project's 
-build directory. After this point in the CMakeLists.txt file(s), a few variables will be available 
-that can be used to setup your include paths and library linking targets:
-
-.. code-block:: cmake
-
-   include_directories( 
-       ${PacBioBAM_INCLUDE_DIRS} 
-       # other includes that your project needs
-   )
-
-   add_executable(foo)
-   
-   target_link_libraries(foo 
-       ${PacBioBAM_LIBRARIES}
-       # other libs that your project needs
-   )
-
-Non-CMake projects
-``````````````````
-
-If you're using something other than CMake for your project's build system, then you need to point 
-it to pbbam's include directory & library, as well as those of its dependencies (primarily htslib).
-
-If you built and installed pbbam using Meson, pkg-config files will be available to be consumed by
-projects wishing to utilize pbbam. Autoconf, CMake, Waf, SCons and Meson all have means to determine
+If you built and installed pbbam, pkg-config files will be available to be consumed by projects
+wishing to utilize pbbam. Autoconf, CMake, Waf, SCons and Meson all have means to determine
 dependency information from pkg-config files.

docs/source/swig_bindings.rst

-.. _swig_bindings:
-
-Additional Languages
-====================
-
-pbbam uses SWIG to generate bindings for other languages. Currently this includes support for C#, Python, and R.
-
-These bindings are disabled by default. See the entry below for your target language to configure pbbam & integrate
-the bindings into your project.
-
-.. _swig_bindings-csharp:
-
-C#
-------
-
-Building
-````````
-
-To build the support for C#, you need to tell CMake to enable it before building:
-
-.. code-block:: console
-
-   $ cmake .. -DPacBioBAM_wrap_csharp
-   $ make
-
-The 'make' step will build relevant libraries/wrappers, and then run a simple program using them, 
-as a quick sanity-check. 
-
-After building, the libraries and wrappers can be found under the pbbam/lib/csharp directory. 
-
-API Example
-```````````
-
-.. code-block:: c#
-
-   using PacBio.BAM;
-
-   namespace TestStuff
-   {
-       public class TestPbbam
-       {
-           public static void TestZmwQuery()
-           {
-               var d = new DataSet("foo.bam");
-               var q = new ZmwQuery(new IntList {1, 2, 3}, d);
-               var q2 = new ZmwQuery(new IntList { 14743 }, d);
-               if (0 != q.Count() || 4 != q2.Count())
-               {
-                   throw new Exception("ZmwQuery not working");
-               }
-               Console.WriteLine("TestZmwQuery - OK!");
-           }
-       }
-   }
-
-.. _swig_bindings-python:
-
-Python
-------
-
-Building
-````````
-
-To build the support for Python, you need to tell CMake to enable it:
-
-.. code-block:: console
-
-   $ cmake .. -DPacBioBAM_wrap_python
-   $ make
-
-The 'make' step will build relevant libraries/wrappers, and then run a simple program using them, 
-as a quick sanity-check. 
-
-After building, the libraries and wrappers can be found in the pbbam/lib/python directory. 
-'make test' will also include some Python-side unit tests as well.
-
-To use the PacBioBam module, you can set your PYTHONPATH before invoking your script:
-
-.. code-block:: console
-
-   $ PYTHONPATH="path/to/pbbam/lib/python" python myScript.py
-
-Or otherwise configure your environment to find the PacBioBam module. 
-
-API Example
-```````````
-
-.. code-block:: python
-
-   import PacBioBam
-   
-   try:
-       file = PacBioBam.BamFile('foo.bam')
-       writer = PacBioBam.BamWriter('new.bam', file.Header())
-       dataset = PacBioBam.DataSet(file)
-       entireFile = PacBioBam.EntireFileQuery(dataset)
-       for record in PacBioBam.Iterate(entireFile):
-           writer.Write(record)
-   except RuntimeError:
-       # found error
-   
-Python-Specific Notes
-`````````````````````
-   
-Iteration
-.........
-
-Iteration over dataset queries in Python will likely need to use the PacBioBam.Iterate() method. Thus
-file iteration loops will look something like the following:
-
-.. code-block:: python
-       
-   entireFile = PacBioBam.EntireFileQuery("input.bam")
-   for record in PacBioBam.Iterate(entireFile):
-       foo.bar(record)
-
-Exception Handling
-..................
-   
-Exceptions are used widely by the C++ library. To handle them from Python, you can use try blocks, looking for
-any RuntimeError:
-
-.. code-block:: python
-
-   try:
-       file = PacBioBam.BamFile("does_not_exist.bam")
-   except RuntimeError: 
-       print("caught expected error")
-   
-.. _swig_bindings-r:
-
-R
-------
-
-Building
-````````
-
-To build the support for R, you need to tell CMake to enable it:
-
-.. code-block:: console
-
-   $ cmake .. -DPacBioBAM_wrap_r
-   $ make
-   
-The 'make' step will build relevant libraries/wrappers, and then run a simple program using them, 
-as a quick sanity-check. 
-
-After building, the libraries and wrappers can be found in the pbbam/lib/R directory. 
-'make test' will also include some R-side unit tests as well.   
-
-To use the PacBioBam module in your script, nothing should be needed up front - simply invoke 'R' as normal. 
-You'll do the dynamic load of the R module near the beginning of your script:
-
-.. code-block:: r
-
-   # load pbbam R library
-   lib_path <- "path/to/pbbam/lib/R"
-   pbbam_libname <- paste(lib_path, "PacBioBam",   sep="/")
-   pbbam_wrapper <- paste(lib_path, "PacBioBam.R", sep="/")
-   dyn.load(paste(pbbam_libname, .Platform$dynlib.ext, sep=""))
-   source(pbbam_wrapper)
-   cacheMetaData(1) 
-
-
-API Example
-```````````
-
-.. code-block:: r
-
-   # load pbbam R library
-   lib_path <- "path/to/pbbam/lib/R"
-   pbbam_libname <- paste(lib_path, "PacBioBam",   sep="/")
-   pbbam_wrapper <- paste(lib_path, "PacBioBam.R", sep="/")
-   dyn.load(paste(pbbam_libname, .Platform$dynlib.ext, sep=""))
-   source(pbbam_wrapper)
-   cacheMetaData(1)    
-  
-   # sample method
-   copyFileAndFetchRecordNames <-function(inputFn, outputFn) {
-	
-       result <- tryCatch(
-       {
-           file   <- BamFile(inputFn)
-           writer <- BamWriter(outputFn, file$Header())
-           ds     <- DataSet(file)
-            
-           entireFile <- EntireFileQuery(ds)
-           iter <- entireFile$begin()
-           end  <- entireFile$end()
-   			
-           while ( iter$'__ne__'(end) ) {
-               record <- iter$value()
-                
-               names_in <- c(names_in, record$FullName())
-               writer$Write(record)
-               iter$incr()
-            }
-            writer$TryFlush()
-            return(names_in)
-        },
-        error = function(e) {
-            # handle error 
-            return(list())
-        })
-        return(result)
-   }
-
-R-Specific Notes
-````````````````
-
-Iteration
-.........
-
-To compare iterators, you'll need to explicitly use the '__eq__' or '__ne__' methods. Thus iterating over
-a data query, will look something like this:
-
-.. code-block:: r
-
-   iter <- query$begin()
-   end  <- query$end()
-   while ( iter$'__ne__'(end) ) {
-       record <- iter$value() 
-       
-       # do stuff with record
-   }
-   
-operator[]
-..........  
-   
-In C++, operator[] can be used in some classes to directly access elements in a sequence, e.g. Cigar string
-
-.. code-block:: cpp
-
-   CigarOperation op = cigar[0]; 
-   
-For the R wrapper, if you want to do the same sort of thing, you'll need to use the '__getitem__' method. 
-Please note that these are **0-based** indices, not 1-based as in much of R. 
-
-.. code-block:: r
-
-   op <- cigar$'__getitem__'(0) 
-   
-Exception Handling
-..................
-
-Exceptions are used widely by the C++ library. To handle them from R, you can use the 'tryCatch' block, listening for 
-'error' type exceptions.
-
- .. code-block:: r
- 
-    result <- tryCatch(
-    {
-        f <- BamFile("does_not_exist.bam") # this statement will throw
-    },
-    error = function(e) {
-        print(paste("caught expected erorr: ",e))
-    })

docs/specs/pbbam.rst

@@ -164,7 +164,7 @@ Output PacBio BAMs will be compatible with the `PacBio BAM`_ specification (2)
 and thus compatible with the general `BAM format`_ specification (1). This
 ensures that a wide variety of downstream tools can interact with data files.
 
-The software uses `CMake`_ as its build system.
+The software uses `Meson`_ as its build system.
 
 The core C++ API relies on the following 3rd party components:
 
@@ -176,7 +176,7 @@ Wrapper APIs for additional languages (Python, R, C#) are generated by `SWIG`_.
 
 API documentation is generated via `Doxygen`_.
 
-.. _CMake: https://cmake.org/
+.. _Meson: https://mesonbuild.com
 .. _zlib: http://www.zlib.net/
 .. _htslib: https://github.com/samtools/htslib
 .. _Boost: http://www.boost.org/
@@ -454,7 +454,7 @@ Analysis subsystem. See `SMRT Analysis`_ (6) specifications for more detail.
 
 Additionally, the library may be built independently, either from internal
 version control (Perforce) or from the public-facing Github repository. In
-either case, `CMake`_ is used to drive the build process.
+either case, `Meson`_ is used to drive the build process.
 
 6.7. Administration
 -------------------
@@ -537,9 +537,8 @@ operating system (Linux distributions, Apple OSX, etc.).
 8.5. SOUP Components
 --------------------
 
-pbbam utilizes CMake for its build system. The C++ library uses the following
-3rd-party software components: Boost, htslib, & zlib. Wrappers for additional
-languages are generated using SWIG.
+pbbam utilizes Meson for its build system. The C++ library uses the following
+3rd-party software components: Boost, htslib and zlib.
 
 8.6. Deployment and Configuration
 ---------------------------------

include/meson.build

@@ -9,6 +9,7 @@ if not meson.is_subproject()
       'pbbam/AlignmentPrinter.h',
       'pbbam/BaiIndexedBamReader.h',
       'pbbam/BamFile.h',
+      'pbbam/BamFileMerger.h',
       'pbbam/BamHeader.h',
       'pbbam/BamReader.h',
       'pbbam/BamRecord.h',
@@ -30,11 +31,14 @@ if not meson.is_subproject()
       'pbbam/DataSetTypes.h',
       'pbbam/DataSetXsd.h',
       'pbbam/EntireFileQuery.h',
+      'pbbam/FastaCache.h',
       'pbbam/FastaReader.h',
       'pbbam/FastaSequence.h',
       'pbbam/FastaSequenceQuery.h',
+      'pbbam/FastaWriter.h',
       'pbbam/FastqReader.h',
       'pbbam/FastqSequence.h',
+      'pbbam/FastqWriter.h',
       'pbbam/FrameEncodingType.h',
       'pbbam/Frames.h',
       'pbbam/GenomicInterval.h',
@@ -91,43 +95,17 @@ if not meson.is_subproject()
 
   install_headers(
     files([
-      'pbbam/internal/Accuracy.inl',
-      'pbbam/internal/BamHeader.inl',
-      'pbbam/internal/BamRecord.inl',
-      'pbbam/internal/BamRecordBuilder.inl',
-      'pbbam/internal/BamRecordImpl.inl',
-      'pbbam/internal/BamRecordView.inl',
-      'pbbam/internal/Cigar.inl',
-      'pbbam/internal/CigarOperation.inl',
       'pbbam/internal/Compare.inl',
       'pbbam/internal/CompositeBamReader.inl',
-      'pbbam/internal/CompositeFastaReader.inl',
-      'pbbam/internal/DataSet.inl',
       'pbbam/internal/DataSetBaseTypes.h',
-      'pbbam/internal/DataSetBaseTypes.inl',
       'pbbam/internal/DataSetElement.h',
       'pbbam/internal/DataSetElement.inl',
-      'pbbam/internal/DataSetListElement.h',
-      'pbbam/internal/DataSetListElement.inl',
-      'pbbam/internal/DataSetTypes.inl',
-      'pbbam/internal/FastaSequence.inl',
-      'pbbam/internal/FastqSequence.inl',
-      'pbbam/internal/Frames.inl',
-      'pbbam/internal/GenomicInterval.inl',
       'pbbam/internal/Interval.inl',
       'pbbam/internal/PbiBasicTypes.inl',
       'pbbam/internal/PbiFilter.inl',
       'pbbam/internal/PbiFilterTypes.inl',
-      'pbbam/internal/PbiRawData.inl',
-      'pbbam/internal/ProgramInfo.inl',
-      'pbbam/internal/QualityValue.inl',
-      'pbbam/internal/QualityValues.inl',
       'pbbam/internal/QueryBase.h',
-      'pbbam/internal/QueryBase.inl',
-      'pbbam/internal/ReadGroupInfo.inl',
-      'pbbam/internal/SequenceInfo.inl',
-      'pbbam/internal/Tag.inl',
-      'pbbam/internal/Validator.inl']),
+      'pbbam/internal/QueryBase.inl']),
     subdir : 'pbbam/internal')
 
   install_headers(
@@ -143,14 +121,6 @@ if not meson.is_subproject()
       'pbbam/vcf/VcfWriter.h']),
     subdir : 'pbbam/vcf')
 
-  install_headers(
-    files([
-      'pbbam/vcf/internal/VcfVariant.inl',
-      'pbbam/vcf/internal/VcfFile.inl',
-      'pbbam/vcf/internal/VcfHeader.inl',
-      'pbbam/vcf/internal/VcfHeaderTypes.inl']),
-    subdir : 'pbbam/vcf/internal')
-
   install_headers(
     files([
       'pbbam/virtual/VirtualPolymeraseBamRecord.h',

include/pbbam/Accuracy.h

@@ -34,11 +34,11 @@ public:
     ///
     Accuracy(float accuracy);
 
-    Accuracy(const Accuracy&) = default;
-    Accuracy(Accuracy&&) = default;
-    Accuracy& operator=(const Accuracy&) = default;
-    Accuracy& operator=(Accuracy&&) = default;
-    ~Accuracy() = default;
+    Accuracy(const Accuracy&);
+    Accuracy(Accuracy&&);
+    Accuracy& operator=(const Accuracy&);
+    Accuracy& operator=(Accuracy&&);
+    ~Accuracy();
 
     /// \}
 
@@ -53,6 +53,4 @@ private:
 }  // namespace BAM
 }  // namespace PacBio
 
-#include "pbbam/internal/Accuracy.inl"
-
 #endif  // ACCURACY_H