Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/.gitignore
+++ b/.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
--- a/CHANGELOG.md
+++ b/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

--- a/CMakeLists.txt
+++ b/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)
--- a/bamboo_build.sh
+++ b/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
--- a/bamboo_build_itg.sh
+++ b/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
--- a/bamboo_build_pa.sh
+++ b/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
--- a/bamboo_coverage.sh
+++ b/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 "${PREFIX_ARG:-/usr/local}" \
-  -Db_coverage=true \
-  ..
-
-ninja test
-
-echo "################"
-echo "# COVERAGE     #"
-echo "################"
-
-find . -type f -iname '*.o' | xargs gcov -acbrfu {} \; >/dev/null && \
-mkdir coverage && pushd coverage && mv ../*.gcov . && \
-sed -i -e 's@Source:@Source:../@' *.gcov && \
-sed -i -e 's@Graph:@Graph:../@' *.gcov && \
-sed -i -e 's@Data:@Data:../@' *.gcov && \
-rm pugixml*
-
--- a/cmake/FindHTSlib.cmake
+++ b/cmake/FindHTSlib.cmake
-# Find HTSlib
-find_package(PkgConfig REQUIRED)
-pkg_check_modules(HTSlib REQUIRED htslib)
-
-# because CMake is trying to be extra clever,
-# it will not properly load libraries with
-# absolute paths in *_LIBRARIES
-set(HTSlib_LIBRARIES "${HTSlib_LDFLAGS}")
-
-message(STATUS "   HTSlib include dirs: ${HTSlib_INCLUDE_DIRS}")
-message(STATUS "   HTSlib libraries: ${HTSlib_LIBRARIES}")
--- a/cmake/PbbamTool.cmake
+++ b/cmake/PbbamTool.cmake
-include(CMakeParseArguments)
-
-function(create_pbbam_tool)
-
-    # parse args
-    set(oneValueArgs TARGET)
-    set(multiValueArgs SOURCES)
-    cmake_parse_arguments(create_pbbam_tool "" "${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)
--- a/cmake/pbbam-ccache.cmake
+++ b/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()
--- a/cmake/pbbam-compilerflags.cmake
+++ b/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()
--- a/cmake/pbbam-dependencies.cmake
+++ b/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()
--- a/cmake/pbbam-libtype.cmake
+++ b/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()
-
-
-
--- a/debian/changelog
+++ b/debian/changelog
+pbbam (0.23.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * Afif removed himself from Uploaders
+  * Add myself to Uploaders
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Set upstream metadata fields: Contact, Name.
+  * Rename library to libpbbam0.23.0 due to upstream choice of ABI version
+  * Remove code copy of python-cram from upstream source
+  * Build-Depends: python3-cram
+  * d/control: Use <!nocheck> instead of comment
+
+ -- Andreas Tille <tille@debian.org>  Sun, 04 Aug 2019 09:15:35 +0200
+
 pbbam (0.19.0+dfsg-4) unstable; urgency=medium

  * Team upload.

--- a/debian/compat
+++ b/debian/compat
-12
--- a/debian/control
+++ b/debian/control
 Source: pbbam
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
               dh-exec,
               d-shlibs,
               meson,
               pkg-config,
-               python,
 # swig3.0,
-               libboost-dev (>= 1.54),
+               libboost-dev,
               zlib1g-dev,
               libssl-dev,
               libhts-dev,
-# Test-Depends:
-               libgtest-dev,
-               python-cram,
-               samtools
-Standards-Version: 4.3.0
+               libgtest-dev <!nocheck>,
+               python3-cram <!nocheck>,
+               samtools <!nocheck>
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/pbbam
 Vcs-Git: https://salsa.debian.org/med-team/pbbam.git
 Homepage: http://pbbam.readthedocs.org/en/latest/index.html
@@ -26,7 +25,7 @@ Package: pbbamtools
 Architecture: any
 Depends: ${shlibs:Depends},
         ${misc:Depends},
-         libpbbam0.19.0 (= ${binary:Version})
+         libpbbam0.23.0 (= ${binary:Version})
 Recommends: samtools
 Description: processing Pacific Biosciences binary alignment/map files
 The BAM format is a binary, compressed, record-oriented container format
@@ -41,7 +40,7 @@ Description: processing Pacific Biosciences binary alignment/map files
 This package provides command-line utilities for working with PacBio BAM
 files.

-Package: libpbbam0.19.0
+Package: libpbbam0.23.0
 Architecture: any
 Multi-Arch: same
 Section: libs
@@ -64,7 +63,7 @@ Description: Pacific Biosciences binary alignment/map (BAM) library
 Package: libpbbam-dev
 Architecture: any
 Section: libdevel
-Depends: libpbbam0.19.0 (= ${binary:Version}),
+Depends: libpbbam0.23.0 (= ${binary:Version}),
         libhts-dev,
         libssl-dev,
         ${misc:Depends}

--- a/debian/copyright
+++ b/debian/copyright
@@ -4,6 +4,7 @@ Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
 Source: https://github.com/PacificBiosciences/pbbam
 Files-Excluded: third-party
                */clang-format*
+                */tests/scripts/cram*

 Files: *
 Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>

--- a/debian/patches/python3.patch
+++ b/debian/patches/python3.patch
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 04 Aug 2019 09:15:35 +0200
+Description: Use Python3 in build time test suite
+
+--- a/meson.build
+++ b/meson.build
+@@ -80,7 +80,7 @@ subdir('src')
+ 
+ if not meson.is_subproject()
+   if get_option('build-tools') or get_option('tests')
+-    pbbam_python = find_program('python')
+    pbbam_python = find_program('python3')
+ 
+     if get_option('tests')
+       pbbam_clang_formatter = find_program('tools/check-formatting')
+--- a/tests/scripts/generate_data.py
+++ b/tests/scripts/generate_data.py
+@@ -1,7 +1,4 @@
+-#!/usr/bin/env python
+-
+-from __future__ import print_function
+-from __future__ import unicode_literals
+#!/usr/bin/python3
+ 
+ import os, shutil, sys
+ from io import StringIO
+@@ -177,9 +174,9 @@ class TestDataGenerator:
+         # else silent success
+         if self.outputFiles or self.outputSymlinks:
+             print('Generating test data in %s ' % self.generatedDataDir)
+-            for file, func in self.outputFiles.items():
+            for file, func in list(self.outputFiles.items()):
+                 func(file)
+-            for link, func in self.outputSymlinks.items():
+            for link, func in list(self.outputSymlinks.items()):
+                 func(link)
+ 
+ # script entry point
--- a/debian/patches/series
+++ b/debian/patches/series
 fix_gtest_depcheck.patch
 # debug_tests.patch
+use_debian_packaged_python3-cram.patch
+python3.patch
--- a/debian/patches/use_debian_packaged_python3-cram.patch
+++ b/debian/patches/use_debian_packaged_python3-cram.patch
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 04 Aug 2019 09:15:35 +0200
+Description: Use python3-cram instead of cram code copy
+
+--- a/tests/meson.build
+++ b/tests/meson.build
+@@ -1,6 +1,6 @@
+ subdir('src')
+ 
+-pbbam_cram_script = find_program('cram', required : false)
+pbbam_cram_script = find_program('cram3', required : false)
+ if not pbbam_cram_script.found()
+   warning('Using bundled cram script')
+   pbbam_cram_script = find_program('scripts/cram.py', required : true)