.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

@@ -14,3 +14,6 @@ tests/bin/test_pbbam
 tests/data/test_group_query/group.fofn
 tests/src/TestData.h
 
+# Meson WrapDB stuff
+subprojects/packagecache/
+subprojects/googletest*

.travis.yml

@@ -34,9 +34,6 @@ before_install:
   # prep zlib
   - sudo apt-get install -y -qq zlib1g-dev
 
-  # prep htslib
-  - "cd .. && git clone https://github.com/PacificBiosciences/htslib.git && cd htslib && make && sudo make install; cd $TRAVIS_BUILD_DIR"
-
   # prep GoogleTest 
   - sudo apt-get install -y -qq libgtest-dev
 

CHANGELOG.md

@@ -10,8 +10,123 @@ guarantees will be maintained within each major version series.
 
 ## Active
 
+## [0.17.0] - 2018-03-18
+
+### Added
+- CompressionLevel/NumThreads parameter implementation to PbiBuilder.
+- Dataset ctor to PbiFileQuery.
+- TranscriptSet to XML support.
+- Auto-enabled "permissive CIGAR mode" for pbbamify tool.
+- IndexedBamWriter, for more efficient writing of BAM & PBI simultaneously.
+
+## [0.16.0] - 2018-01-17
+
+### Removed
+- Removed the PbiIndex class and its "lookup data"-related helpers. These were 
+never as useful as initially intended. PbiRawData and its related classes are the 
+recommended interface for working with PBI index data.
+
+## [0.15.0] - 2018-01-12
+
+### Added
+- Support for long CIGARs (>64K operations).
+
+## [0.14.0] - 2017-12-12
+
+### Added
+- Support for newer style QNAMEs. Recent version of htslib (1.4+) have started
+adding extra null terminators to make the subsequent CIGAR section 32-bit aligned.
+
+### Changed
+- Requirements for htslib version used. Must now be htslib v1.4+.
+
+## [0.13.2] - 2017-09-25
+
+### Added
+- Backward compatibility for C++11 (std::make_unique which is 11/14 agnostic).
+
+## [0.13.1] - 2017-09-25
+
+### Added
+- Support for "pe" tag in stitched, virtual reads. 
+
+## [0.13.0] - 2017-09-25
+
+### Changed
+- Ran clang-tidy (modernize) over codebase to clean up legacy coding styles.
+
+## [0.12.2] - 2017-09-22
+
+### Added 
+- HasPulseExclusion() to BamRecord (& derived types). 
+
+## [0.12.1] - 2017-09-21
+
+### Added
+- Pulse exclusion base feature to read group.
+
+## [0.12.0] - 2017-09-19
+
+### Added
+- NumReads() for PBI filter-based queries. This allows fetching of the number
+of reads that pass the filter, without needing to iterate over the entire 
+file(s).
+
+## [0.11.0] - 2017-09-15
+
+### Added
+- Support for internal tag: pulse exclusion reason ("pe"). New methods on 
+BamRecord, and new enum PulseExclusionReason.
+
+### Changed
+- Default PacBioBAM format version now 3.0.5
+
+## [0.10.2] - 2017-09-14
+
+### Changed
+- Explicitly trim all whitespace from FASTA input.
+
+## [0.10.1] - 2017-09-11
+
+### Changed
+- Frames, add mutex to avoid race condition in InitIpdDownsampling(void)
+
+## [0.10.0] - 2017-09-08
+
+### Changed
+- PbiBuilder backend for generating PBI index files "on-the-fly" along with
+writing BAM files. The previous implementation's memory usage scaled linearly 
+with the number of reads, sometimes reaching huge numbers (several gigs or more).
+The new implementation's memory usage remains constant for any number of reads, 
+without any runtime hit on files/architectures tested. 
+
+### Removed
+- PbiBuilder::Result(). Returned an intermediate snapshot of the index under
+construction. This method isn't usable with the new PbiBuilder backend and was 
+really only useful for initial debugging/testing. It is no longer used in the 
+test framework and is unlikely to be used by client code either. Dropping this 
+method from the API, and thus bumping the version number. 
+
+## [0.9.0] - 2017-08-07
+
+### Removed
+- Bundled htslib. Now using 'stock' htslib (v1.3.1+).
+- Built-in SWIG wrappers. 
+
+## [0.8.0] - 2017-07-24
+
 ### Added
 - Default DataSet 'Version' attribute if none already present (currently 4.0.0)
+- Added whitelist support for filtering ZMWs via DataSetXML.
+- Added iterable query over FASTA files & ReferenceSet datasets.
+- Added DataSet::AllFiles to access primary resources AND their child files (indices,
+scraps, etc).
+
+### Fixed
+- Bug in the build system preventing clean rebuilds.
+
+### Removed
+- Dropped the bundled, PacBio-forked version of htslib. Now using stock htslib (v1.3.1+). 
 
 ## [0.7.4] - 2016-11-18
 

CMakeLists.txt

@@ -3,7 +3,7 @@
 ########################################################################
 
 cmake_policy(SET CMP0048 NEW)  # lets us set version in project()
-project(PacBioBAM VERSION 0.7.4 LANGUAGES CXX C)
+project(PacBioBAM VERSION 0.17.0 LANGUAGES CXX C)
 cmake_minimum_required(VERSION 3.0)
 
 # project name & version
@@ -17,39 +17,32 @@ option(PacBioBAM_build_docs    "Build PacBioBAM's API documentation."
 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_wrap_csharp   "Build PacBioBAM with SWIG bindings for C#."             OFF)
-option(PacBioBAM_wrap_python   "Build PacBioBAM with SWIG bindings for Python."         OFF)
-option(PacBioBAM_wrap_r        "Build PacBioBAM with SWIG bindings for R."              OFF)
 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_wrap_csharp OR PacBioBAM_wrap_r OR PacBioBAM_wrap_python)
-    set(wrapping_swig TRUE)
-else()
-    set(wrapping_swig FALSE)
-endif()
-
 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_SwigSourceDir ${PacBioBAM_RootDir}/src/swig)
 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 ${CMAKE_CURRENT_BINARY_DIR})
-else()
-    if(${wrapping_swig})
-        message(FATAL_ERROR "SWIG bindings not currently supported in modular build.")
-    endif()
 endif()
 set(PacBioBAM_BinDir    ${PacBioBAM_OutputDir}/bin)
 set(PacBioBAM_LibDir    ${PacBioBAM_OutputDir}/lib)

LICENSE.txt

-Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+Copyright (c) 2014-2018, Pacific Biosciences of California, Inc.
 
 All rights reserved.
 

README.md

@@ -23,7 +23,40 @@ This library is **not** intended to be used as a general-purpose BAM utility - a
 
   - [Changelog](https://github.com/PacificBiosciences/pbbam/blob/master/CHANGELOG.md)
 
+## FAQ
+
+### [Help! I am getting "unsupported sequencing chemistry combination"!](#chemistry-bundle)
+
+**pbbam** validates all BAM files, and as part of this validation, it checks whether the
+`BindingKit` and `SequencingKit` variables in every ReadGroup of the provided BAM file are
+known. As part of ongoing chemistry developments, we might need to introduce new part numbers
+to identify novel reagents and/or SMRT Cells. You are unlikely to encounter such issues
+when using SMRT Link, as it has an integrated auto-updater that will periodically check and
+install new chemistries automatically. All PacBio tools being used without a proper SMRT Link
+installation will require manual intervention to download new chemistries:
+
+  ```sh
+  cd <some persistent dir>
+  export SMRT_CHEMISTRY_BUNDLE_DIR="${PWD}"
+
+  wget https://raw.githubusercontent.com/PacificBiosciences/pbcore/develop/pbcore/chemistry/resources/mapping.xml -O chemistry.xml
+  ```
+
+This will cause **pbbam** to try to load the out-of-band `chemistry.xml` from
+`SMRT_CHEMISTRY_BUNDLE_DIR` and should allow you to use somewhat older software
+with somewhat newer BAMs. **Note:** this only allows **pbbam**'s internal validation
+to pass, this will not automatically make other chemistry-dependent software work
+with newer chemistries. For instance, Arrow's backend ([Unanimity](https://github.com/PacificBiosciences/unanimity))
+is parametrized on chemistry too, and it will fail should a completely new chemistry
+be introduced. See Unanimity's FAQ on how to employ `SMRT_CHEMISTRY_BUNDLE_DIR`
+to load models for new chemistries.
+
+
 ## License
 
  - [PacBio open source license](https://github.com/PacificBiosciences/pbbam/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 zlib
+module load htslib
+module load samtools
+
+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
+
+case "${bamboo_planRepository_branchName}" in
+  develop|master)
+    export PREFIX_ARG="/mnt/software/p/pbbam/${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 ${j} gtest
+    fi
+    module load ccache
+
+    export CURRENT_BUILD_DIR="build_unity=${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}
+
+( 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
+
+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

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/FindCSharp.cmake

-#
-# A CMake Module for finding and using C# (.NET and Mono).
-#
-# The following variables are set:
-#   CSHARP_FOUND - set to ON if C# is found
-#   CSHARP_USE_FILE - the path to the C# use file
-#   CSHARP_TYPE - the type of the C# compiler (eg. ".NET" or "Mono")
-#   CSHARP_VERSION - the version of the C# compiler (eg. "v4.0" or "2.10.2")
-#   CSHARP_COMPILER - the path to the C# compiler executable (eg. "C:/Windows/Microsoft.NET/Framework/v4.0.30319/csc.exe" or "/usr/bin/gmcs")
-#   CSHARP_INTERPRETER - the path to interpreter needed to run CSharp executables
-#   CSHARP_PLATFORM - the C# target platform
-#   CSHARP_SDK - the SDK commandline switch (empty for .NET, for Mono eg. "/sdk:2" or "/sdk:4")
-#
-# This file is based on the work of GDCM:
-#   http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/FindCSharp.cmake
-# Copyright (c) 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
-#
-
-# TODO: ADD ABILITY TO SELECT WHICH C# COMPILER eg. .NET or Mono (if both exist). For the moment, .NET is selected above Mono.
-
-# Make sure find package macros are included
-include( FindPackageHandleStandardArgs )
-
-unset( CSHARP_COMPILER CACHE )
-unset( CSHARP_INTERPRETER CACHE )
-unset( CSHARP_TYPE CACHE )
-unset( CSHARP_VERSION CACHE )
-unset( CSHARP_FOUND CACHE )
-
-# By default use anycpu platform, allow the user to override
-set( CSHARP_PLATFORM "anycpu" CACHE STRING "C# target platform: x86, x64, anycpu, or itanium" )
-if( NOT ${CSHARP_PLATFORM} MATCHES "x86|x64|anycpu|itanium" )
-  message( FATAL_ERROR "The C# target platform '${CSHARP_PLATFORM}' is not valid. Please enter one of the following: x86, x64, anycpu, or itanium" )
-endif( )
-
-if( WIN32 )
-  find_package( DotNetFrameworkSdk )
-  if( NOT CSHARP_DOTNET_FOUND )
-    find_package( Mono )
-  endif( )
-else( UNIX )
-  find_package( Mono )
-endif( )
-
-if( CSHARP_DOTNET_FOUND )
-  set( CSHARP_TYPE ".NET" CACHE STRING "Using the .NET compiler" )
-  set( CSHARP_VERSION ${CSHARP_DOTNET_VERSION} CACHE STRING "C# .NET compiler version" FORCE )
-  set( CSHARP_COMPILER ${CSHARP_DOTNET_COMPILER_${CSHARP_DOTNET_VERSION}} CACHE STRING "Full path to .NET compiler" FORCE )
-  set( CSHARP_INTERPRETER "" CACHE INTERNAL "Interpretor not required for .NET" FORCE )
-elseif( CSHARP_MONO_FOUND )
-  set( CSHARP_TYPE "Mono" CACHE STRING "Using the Mono compiler" )
-  set( CSHARP_VERSION ${CSHARP_MONO_VERSION} CACHE STRING "C# Mono compiler version" FORCE )
-  set( CSHARP_COMPILER ${CSHARP_MONO_COMPILER_${CSHARP_MONO_VERSION}} CACHE STRING "Full path to Mono compiler" FORCE )
-  set( CSHARP_INTERPRETER ${CSHARP_MONO_INTERPRETER_${CSHARP_MONO_VERSION}} CACHE STRING "Full path to Mono interpretor" FORCE )
-  set( CSHARP_SDK "/sdk:4.5" CACHE STRING "C# Mono SDK commandline switch (e.g. /sdk:2, /sdk:4, /sdk:5)" )
-endif( )
-
-# Handle WIN32 specific issues
-if ( WIN32 )
-  if ( CSHARP_COMPILER MATCHES "bat" )
-    set( CSHARP_COMPILER "call ${CSHARP_COMPILER}" )
-  endif ( )
-endif( )
-
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(CSharp DEFAULT_MSG CSHARP_TYPE CSHARP_VERSION CSHARP_COMPILER)
-
-mark_as_advanced( CSHARP_TYPE CSHARP_VERSION CSHARP_COMPILER CSHARP_INTERPRETER CSHARP_PLATFORM CSHARP_SDK )
-
-# Set the USE_FILE path
-# http://public.kitware.com/Bug/view.php?id=7757
-get_filename_component( current_list_path ${CMAKE_CURRENT_LIST_FILE} PATH )
-set( CSHARP_USE_FILE ${current_list_path}/UseCSharp.cmake )

cmake/FindDotNetFrameworkSdk.cmake

-# Set paths and vars for .NET compilers 
-# This is hand-rolled because I had problems with the one from SimpleITK
-
-#
-# The following variables are set:
-#   CSHARP_DOTNET_FOUND
-#   CSHARP_DOTNET_COMPILER_${version} eg. "CSHARP_DOTNET_COMPILER_v4.0.30319"
-#   CSHARP_DOTNET_VERSION eg. "v4.0.30319"
-#   CSHARP_DOTNET_VERSIONS eg. "v2.0.50727, v3.5, v4.0.30319"
-#   DotNetFrameworkSdk_USE_FILE
-#
-#   CSHARP_PROJECT_BUILDER (xbuild/msbuild)
-
-set(framework_dir "C:/Windows/Microsoft.NET/Framework")
-
-set(CSHARP_DOTNET_VERSION "v4.0.30319")
-set(CSHARP_DOTNET_VERSIONS "")
-set(CSHARP_DOTNET_COMPILER_${CSHARP_DOTNET_VERSION} "${framework_dir}/${CSHARP_DOTNET_VERSION}/csc.exe")
-set(CSHARP_PROJECT_BUILDER "${framework_dir}/${CSHARP_DOTNET_VERSION}/MSBuild.exe")
-
-if(EXISTS ${CSHARP_DOTNET_COMPILER_${CSHARP_DOTNET_VERSION}})
-	set(CSHARP_DOTNET_FOUND 1)
-else()
-	set(CSHARP_DOTNET_FOUND 0)
-endif()
-
-# Set USE_FILE
-get_filename_component( current_list_path ${CMAKE_CURRENT_LIST_FILE} PATH )
-set( DotNetFrameworkSdk_USE_FILE ${current_list_path}/UseDotNetFrameworkSdk.cmake )
\ No newline at end of file

cmake/FindMono.cmake

-#
-# A CMake Module for finding Mono.
-#
-# The following variables are set:
-#   CSHARP_MONO_FOUND
-#   CSHARP_MONO_COMPILER_${version} eg. "CSHARP_MONO_COMPILER_2.10.2"
-#   CSHARP_MONO_INTERPRETOR_${version} eg. "CSHARP_MONO_INTERPRETOR_2.10.2"
-#   CSHARP_MONO_VERSION eg. "2.10.2"
-#   CSHARP_MONO_VERSIONS eg. "2.10.2, 2.6.7"
-#
-# Additional references can be found here:
-#   http://www.mono-project.com/Main_Page
-#   http://www.mono-project.com/CSharp_Compiler
-#   http://mono-project.com/FAQ:_Technical (How can I tell where the Mono runtime is installed)
-#
-# This file is based on the work of GDCM:
-#   http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/FindMono.cmake
-# Copyright (c) 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
-#
-
-set( csharp_mono_valid 1 )
-if( DEFINED CSHARP_MONO_FOUND )
-  # The Mono compiler has already been found
-  # It may have been reset by the user, verify it is correct
-  if( NOT DEFINED CSHARP_MONO_COMPILER_${CSHARP_MONO_VERSION} )
-    set( csharp_mono_version_user ${CSHARP_MONO_VERSION} )
-    set( csharp_mono_valid 0 )
-    set( CSHARP_MONO_FOUND 0 )
-    set( CSHARP_MONO_VERSION "CSHARP_MONO_VERSION-NOTVALID" CACHE STRING "C# Mono compiler version, choices: ${CSHARP_MONO_VERSIONS}" FORCE )
-    message( FATAL_ERROR "The C# Mono version '${csharp_mono_version_user}' is not valid. Please enter one of the following: ${CSHARP_MONO_VERSIONS}" )
-  endif( NOT DEFINED CSHARP_MONO_COMPILER_${CSHARP_MONO_VERSION} )
-endif( DEFINED CSHARP_MONO_FOUND )
-
-unset( CSHARP_MONO_VERSIONS CACHE ) # Clear versions
-if( WIN32 )
-  # Search for Mono on Win32 systems
-  # See http://mono-project.com/OldReleases and http://www.go-mono.com/mono-downloads/download.html
-  set( csharp_mono_bin_dirs )
-  set( csharp_mono_search_hints
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.11.2;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.9;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.8;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.7;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.6;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.5;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.4;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.3;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.2;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10.1;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.10;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.8;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.6.7;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.6.4;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.6.3;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.6.1;SdkInstallRoot]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono\\2.6;SdkInstallRoot]/bin"
-  )
-  foreach( csharp_mono_search_hint ${csharp_mono_search_hints} )
-    get_filename_component( csharp_mono_bin_dir "${csharp_mono_search_hint}" ABSOLUTE )
-    if ( EXISTS "${csharp_mono_bin_dir}" )
-      set( csharp_mono_bin_dirs ${csharp_mono_bin_dirs} ${csharp_mono_bin_dir} )
-    endif ( EXISTS "${csharp_mono_bin_dir}" )
-  endforeach( csharp_mono_search_hint )
-  # TODO: Use HKLM_LOCAL_MACHINE\Software\Novell\Mono\DefaultCLR to specify default version
-  # get_filename_component( test "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Novell\\Mono;DefaultCLR]" NAME )
-
-  foreach ( csharp_mono_bin_dir ${csharp_mono_bin_dirs} )
-    string( REPLACE "\\" "/" csharp_mono_bin_dir ${csharp_mono_bin_dir} )
-    if (EXISTS "${csharp_mono_bin_dir}/dmcs.bat")
-      set( csharp_mono_executable "${csharp_mono_bin_dir}/dmcs.bat")
-    elseif (EXISTS "${csharp_mono_bin_dir}/gmcs.bat")
-      set( csharp_mono_executable "${csharp_mono_bin_dir}/gmcs.bat")
-    elseif (EXISTS "${csharp_mono_bin_dir}/mcs.bat")
-      set( csharp_mono_executable "${csharp_mono_bin_dir}/mcs.bat")
-    endif (EXISTS "${csharp_mono_bin_dir}/dmcs.bat")
-
-    if( csharp_mono_valid )
-      # Extract version number (eg. 2.10.2)
-      string(REGEX MATCH "([0-9]*)([.])([0-9]*)([.]*)([0-9]*)" csharp_mono_version_temp ${csharp_mono_bin_dir})
-      set( CSHARP_MONO_VERSION ${csharp_mono_version_temp} CACHE STRING "C# Mono compiler version" )
-      mark_as_advanced( CSHARP_MONO_VERSION )
-
-      # Add variable holding executable
-      set( CSHARP_MONO_COMPILER_${csharp_mono_version_temp} ${csharp_mono_executable} CACHE STRING "C# Mono compiler ${csharp_mono_version_temp}" FORCE )
-      mark_as_advanced( CSHARP_MONO_COMPILER_${csharp_mono_version_temp} )
-
-      # Set interpreter
-      if (EXISTS "${csharp_mono_bin_dir}/mono.exe")
-        set( CSHARP_MONO_INTERPRETER_${csharp_mono_version_temp} "${csharp_mono_bin_dir}/mono.exe" CACHE STRING "C# Mono interpreter ${csharp_mono_version_temp}" FORCE )
-        mark_as_advanced( CSHARP_MONO_INTERPRETER_${csharp_mono_version_temp} )
-      endif (EXISTS "${csharp_mono_bin_dir}/mono.exe")
-    endif( csharp_mono_valid )
-
-    # Create a list of supported compiler versions
-    if( NOT DEFINED CSHARP_MONO_VERSIONS )
-      set( CSHARP_MONO_VERSIONS "${csharp_mono_version_temp}" CACHE STRING "Available C# Mono compiler versions" FORCE )
-    else( NOT DEFINED CSHARP_MONO_VERSIONS )
-      set( CSHARP_MONO_VERSIONS "${CSHARP_MONO_VERSIONS}, ${csharp_mono_version_temp}"  CACHE STRING "Available C# Mono versions" FORCE )
-    endif( NOT DEFINED CSHARP_MONO_VERSIONS )
-    mark_as_advanced( CSHARP_MONO_VERSIONS )
-
-    # We found at least one Mono compiler version
-    set( CSHARP_MONO_FOUND 1 CACHE INTERNAL "Boolean indicating if C# Mono was found" )
-  endforeach( csharp_mono_bin_dir )
-
-else( UNIX )
-  # Search for Mono on non-Win32 systems
-  set( chsarp_mono_names "mcs" "mcs.exe" "dmcs" "dmcs.exe" "smcs" "smcs.exe" "gmcs" "gmcs.exe" )
-  set(
-    csharp_mono_paths
-    "/usr/bin/"
-    "/usr/local/bin/"
-    "/usr/lib/mono/2.0"
-    "/opt/novell/mono/bin"
-  )
-  find_program(
-    csharp_mono_compiler # variable is added to the cache, we removed it below
-    NAMES ${chsarp_mono_names}
-    PATHS ${csharp_mono_paths}
-  )
-
-  if( EXISTS ${csharp_mono_compiler} )
-    # Determine version
-    find_program(
-      csharp_mono_interpreter # variable is added to the cache, we removed it below
-      NAMES mono
-      PATHS ${csharp_mono_paths}
-    )
-    if ( EXISTS ${csharp_mono_interpreter} )
-      execute_process(
-        COMMAND ${csharp_mono_interpreter} -V
-        OUTPUT_VARIABLE csharp_mono_version_string
-      )
-      string( REGEX MATCH "([0-9]*)([.])([0-9]*)([.]*)([0-9]*)" csharp_mono_version_temp ${csharp_mono_version_string} )
-      set( CSHARP_MONO_INTERPRETER_${CSHARP_MONO_VERSION} ${csharp_mono_interpreter} CACHE STRING "C# Mono interpreter ${csharp_mono_version_temp}" FORCE )
-      mark_as_advanced( CSHARP_MONO_INTERPRETER_${CSHARP_MONO_VERSION} )
-    endif ( EXISTS ${csharp_mono_interpreter} )
-    unset( csharp_mono_interpreter CACHE )
-
-    # We found Mono compiler
-    set( CSHARP_MONO_VERSION ${csharp_mono_version_temp} CACHE STRING "C# Mono compiler version" )
-    mark_as_advanced( CSHARP_MONO_VERSION )
-    set( CSHARP_MONO_COMPILER_${CSHARP_MONO_VERSION} ${csharp_mono_compiler} CACHE STRING "C# Mono compiler ${CSHARP_MONO_VERSION}" FORCE )
-    mark_as_advanced( CSHARP_MONO_COMPILER_${CSHARP_MONO_VERSION} )
-    set( CSHARP_MONO_VERSIONS ${CSHARP_MONO_VERSION} CACHE STRING "Available C# Mono compiler versions" FORCE )
-    mark_as_advanced( CSHARP_MONO_VERSIONS )
-    set( CSHARP_MONO_FOUND 1 CACHE INTERNAL "Boolean indicating if C# Mono was found" )
-
-    # Assume xbuild is just xbuild.
-    set(CSHARP_PROJECT_BUILDER "xbuild")
-
-
-  endif( EXISTS ${csharp_mono_compiler} )
-
-  # Remove temp variable from cache
-  unset( csharp_mono_compiler CACHE )
-
-endif( WIN32 )
-
-if( CSHARP_MONO_FOUND )
-  # Report the found versions
-  message( STATUS "Found the following C# Mono versions: ${CSHARP_MONO_VERSIONS}" )
-endif( CSHARP_MONO_FOUND )
-
-# Set USE_FILE
-get_filename_component( current_list_path ${CMAKE_CURRENT_LIST_FILE} PATH )
-set( Mono_USE_FILE ${current_list_path}/UseMono.cmake )

cmake/FindR.cmake

-
-#
-# - This module locates an installed R distribution.
-#
-# Defines the following:
-#
-# R_INCLUDE_DIR      - Path to R include directory
-# R_LIBRARIES        - Path to R library
-# R_LIBRARY_BASE     -
-# R_COMMAND          - Path to R command
-# RSCRIPT_EXECUTABLE - Path to Rscript command
-#
-
-
-# Make sure find package macros are included
-include( FindPackageHandleStandardArgs )
-
-set(TEMP_CMAKE_FIND_APPBUNDLE ${CMAKE_FIND_APPBUNDLE})
-set(CMAKE_FIND_APPBUNDLE "NEVER")
-find_program(R_COMMAND R DOC "R executable.")
-if(R_COMMAND)
-  execute_process(WORKING_DIRECTORY . COMMAND ${R_COMMAND} RHOME OUTPUT_VARIABLE R_BASE_DIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-  set(R_HOME ${R_BASE_DIR} CACHE PATH "R home directory obtained from R RHOME")
-  mark_as_advanced(R_HOME)
-endif(R_COMMAND)
-
-find_program(RSCRIPT_EXECUTABLE Rscript DOC "Rscript executable.")
-
-set(CMAKE_FIND_APPBUNDLE ${TEMP_CMAKE_FIND_APPBUNDLE})
-
-# R.h gets installed in all sorts of places -
-# ubuntu: /usr/share/R/include, RHEL/Fedora: /usr/include/R/R.h
-find_path(R_INCLUDE_DIR R.h PATHS ${R_INCLUDE_DIR_HINT} /usr/local/lib /usr/local/lib64 /usr/share /usr/include ${R_BASE_DIR} PATH_SUFFIXES include R R/include DOC "Path to file R.h")
-find_library(R_LIBRARY_BASE R PATHS ${R_BASE_DIR} PATH_SUFFIXES /lib DOC "R library (example libR.a, libR.dylib, etc.).")
-
-set(R_LIBRARIES ${R_LIBRARY_BASE})
-mark_as_advanced(RSCRIPT_EXECUTABLE R_LIBRARIES R_INCLUDE_DIR R_COMMAND R_LIBRARY_BASE)
-
-
-set( _REQUIRED_R_VARIABLES R_INCLUDE_DIR R_COMMAND )
-
-if( APPLE )
-  # On linux platform some times the libR.so is not available, however
-  # on apple a link error results if the library is linked.
-  list(  APPEND _REQUIRED_R_VARIABLES R_LIBRARIES R_LIBRARY_BASE )
-endif()
-
-find_package_handle_standard_args(R DEFAULT_MSG ${_REQUIRED_R_VARIABLES} )

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/UseCSharp.cmake

-# CMake Module for finding and using C# (.NET and Mono).
-#
-# The following global variables are assumed to exist:
-#   CSHARP_SOURCE_DIRECTORY - path to C# sources
-#   CSHARP_BINARY_DIRECTORY - path to place resultant C# binary files
-#
-# The following variables are set:
-#   CSHARP_TYPE - the type of the C# compiler (eg. ".NET" or "Mono")
-#   CSHARP_COMPILER - the path to the C# compiler executable (eg. "C:/Windows/Microsoft.NET/Framework/v4.0.30319/csc.exe")
-#   CSHARP_VERSION - the version number of the C# compiler (eg. "v4.0.30319")
-#
-# The following macros are defined:
-#   CSHARP_ADD_EXECUTABLE( name references [files] [output_dir] ) - Define C# executable with the given name
-#   CSHARP_ADD_LIBRARY( name references [files] [output_dir] ) - Define C# library with the given name
-#
-# Examples:
-#   CSHARP_ADD_EXECUTABLE( MyExecutable "" "Program.cs" )
-#   CSHARP_ADD_EXECUTABLE( MyExecutable "ref1.dll ref2.dll" "Program.cs File1.cs" )
-#   CSHARP_ADD_EXECUTABLE( MyExecutable "ref1.dll;ref2.dll" "Program.cs;File1.cs" )
-#
-# This file is based on the work of GDCM:
-#   http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/UseCSharp.cmake
-# Copyright (c) 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
-#
-
-# TODO: ADD SUPPORT FOR LINK LIBRARIES
-
-# Check something was found
-if( NOT CSHARP_COMPILER )
-  message( WARNING "A C# compiler executable was not found on your system" )
-endif( NOT CSHARP_COMPILER )
-
-# Include type-based USE_FILE
-if( CSHARP_TYPE MATCHES ".NET" )
-  include( ${DotNetFrameworkSdk_USE_FILE} )
-elseif ( CSHARP_TYPE MATCHES "Mono" )
-  include( ${Mono_USE_FILE} )
-endif ( CSHARP_TYPE MATCHES ".NET" )
-
-macro( CSHARP_ADD_LIBRARY name )
-  CSHARP_ADD_PROJECT( "library" ${name} ${ARGN} )
-endmacro( CSHARP_ADD_LIBRARY )
-
-macro( CSHARP_ADD_EXECUTABLE name )
-  CSHARP_ADD_PROJECT( "exe" ${name} ${ARGN} )
-endmacro( CSHARP_ADD_EXECUTABLE )
-
-# Private macro
-macro( CSHARP_ADD_PROJECT type name )
-  set( refs "/reference:System.dll" )
-  set( sources )
-  set( sources_dep )
-
-  if( ${type} MATCHES "library" )
-    set( output "dll" )
-  elseif( ${type} MATCHES "exe" )
-    set( output "exe" )
-  endif( ${type} MATCHES "library" )
-
-  # Step through each argument
-  foreach( it ${ARGN} )
-    if( ${it} MATCHES "(.*)(dll)" )
-       # Argument is a dll, add reference
-       list( APPEND refs /reference:${it} )
-    else( )
-      # Argument is a source file
-      if( EXISTS ${it} )
-        list( APPEND sources ${it} )
-        list( APPEND sources_dep ${it} )
-      elseif( EXISTS ${CSHARP_SOURCE_DIRECTORY}/${it} )
-        list( APPEND sources ${CSHARP_SOURCE_DIRECTORY}/${it} )
-        list( APPEND sources_dep ${CSHARP_SOURCE_DIRECTORY}/${it} )
-      elseif( ${it} MATCHES "[*]" )
-        # For dependencies, we need to expand wildcards
-        FILE( GLOB it_glob ${it} )
-        list( APPEND sources ${it} )
-        list( APPEND sources_dep ${it_glob} )
-      endif( )
-    endif ( )
-  endforeach( )
-
-  # Check we have at least one source
-  list( LENGTH sources_dep sources_length )
-  if ( ${sources_length} LESS 1 )
-    MESSAGE( SEND_ERROR "No C# sources were specified for ${type} ${name}" )
-  endif ()
-  list( SORT sources_dep )
-
-  # Perform platform specific actions
-  if (WIN32)
-    string( REPLACE "/" "\\" sources ${sources} )
-  else (UNIX)
-    string( REPLACE "\\" "/" sources ${sources} )
-  endif (WIN32)
-
-  # Add custom target and command
-  MESSAGE( STATUS "Adding C# ${type} ${name}: '${CSHARP_COMPILER} /t:${type} /out:${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'" )
-  add_custom_command(
-    COMMENT "Compiling C# ${type} ${name}: '${CSHARP_COMPILER} /t:${type} /out:${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'"
-    OUTPUT ${CSHARP_BINARY_DIRECTORY}/${name}.${output}
-    COMMAND ${CSHARP_COMPILER}
-    ARGS /t:${type} /out:${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}
-    WORKING_DIRECTORY ${CSHARP_BINARY_DIRECTORY}
-    DEPENDS ${sources_dep}
-  )
-  add_custom_target(
-    ${name} ALL
-    DEPENDS ${CSHARP_BINARY_DIRECTORY}/${name}.${output}
-    SOURCES ${sources_dep}
-  )
-endmacro( CSHARP_ADD_PROJECT )

cmake/UseDotNetFrameworkSdk.cmake

-#
-# A CMake Module for using Mono.
-#
-# The following variables are set:
-#   (none)
-#
-# Additional references can be found here:
-#   http://www.mono-project.com/Main_Page
-#   http://www.mono-project.com/CSharp_Compiler
-#
-# This file is based on the work of GDCM:
-#   http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/FindMono.cmake
-# Copyright (c) 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
-#
-
-message( STATUS "Using .NET compiler version ${CSHARP_DOTNET_VERSION}" )
\ No newline at end of file

cmake/UseMono.cmake

-#
-# A CMake Module for using Mono.
-#
-# The following variables are set:
-#   (none)
-#
-# Additional references can be found here:
-#   http://www.mono-project.com/Main_Page
-#   http://www.mono-project.com/CSharp_Compiler
-#
-# This file is based on the work of GDCM:
-#   http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/FindMono.cmake
-# Copyright (c) 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
-#
-
-message( STATUS "Using Mono compiler version ${CSHARP_MONO_VERSION}" )

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()