pax_global_header 0000666 0000000 0000000 00000000064 14600153730 0014511 g ustar 00root root 0000000 0000000 52 comment=b586a268cb27b1dd9ec6283558540d0e4356972d
GenomicsDB-1.5.3/ 0000775 0000000 0000000 00000000000 14600153730 0013471 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.codecov.yml 0000664 0000000 0000000 00000000654 14600153730 0015721 0 ustar 00root root 0000000 0000000 # curl -X POST --data-binary @codecov.yml https://codecov.io/validate
ignore:
- "example/"
- "src/test/"
parsers:
gcov:
branch_detection:
conditional: no
loop: yes
method: no
macro: no
coverage:
range: 50..100
status:
project:
default:
target: auto
threshold: 1.0%
branches: null
patch:
default:
target: auto
branches: null
GenomicsDB-1.5.3/.dockerignore 0000664 0000000 0000000 00000000000 14600153730 0016133 0 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.gitattributes 0000664 0000000 0000000 00000000025 14600153730 0016361 0 ustar 00root root 0000000 0000000 README.md merge=ours
GenomicsDB-1.5.3/.github/ 0000775 0000000 0000000 00000000000 14600153730 0015031 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.github/dependabot.yml 0000664 0000000 0000000 00000001066 14600153730 0017664 0 ustar 00root root 0000000 0000000 # To get started with Dependabot version updates, you'll need to specify which
# package ecosystems to update and where the package manifests are located.
# Please see the documentation for all configuration options:
# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
version: 2
updates:
- package-ecosystem: "maven" # See documentation for possible values
directory: "/" # Location of package manifests
schedule:
interval: "monthly"
target-branch: "develop"
open-pull-requests-limit: 0
GenomicsDB-1.5.3/.github/resources/ 0000775 0000000 0000000 00000000000 14600153730 0017043 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.github/resources/codeql-config.yml 0000664 0000000 0000000 00000000142 14600153730 0022275 0 ustar 00root root 0000000 0000000 name: "CodeQL configuration"
paths-ignore:
- 'dependencies/htslib/'
- 'src/test'
- 'tests'
GenomicsDB-1.5.3/.github/resources/hadoop/ 0000775 0000000 0000000 00000000000 14600153730 0020315 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.github/resources/hadoop/core-site.xml 0000664 0000000 0000000 00000000347 14600153730 0022735 0 ustar 00root root 0000000 0000000
fs.defaultFShdfs://localhost:9000/
GenomicsDB-1.5.3/.github/resources/hadoop/hadoop-env.sh 0000664 0000000 0000000 00000010223 14600153730 0022707 0 ustar 00root root 0000000 0000000 # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Set Hadoop-specific environment variables here.
# The only required environment variable is JAVA_HOME. All others are
# optional. When running a distributed configuration it is best to
# set JAVA_HOME in this file, so that it is correctly defined on
# remote nodes.
# The java implementation to use.
export JAVA_HOME=${JAVA_HOME:-"/usr/java/latest"}
# The jsvc implementation to use. Jsvc is required to run secure datanodes
# that bind to privileged ports to provide authentication of data transfer
# protocol. Jsvc is not required if SASL is configured for authentication of
# data transfer protocol using non-privileged ports.
#export JSVC_HOME=${JSVC_HOME}
export HADOOP_CONF_DIR=${HADOOP_CONF_DIR:-"/etc/hadoop"}
# Extra Java CLASSPATH elements. Automatically insert capacity-scheduler.
for f in $HADOOP_HOME/contrib/capacity-scheduler/*.jar; do
if [ "$HADOOP_CLASSPATH" ]; then
export HADOOP_CLASSPATH=$HADOOP_CLASSPATH:$f
else
export HADOOP_CLASSPATH=$f
fi
done
# The maximum amount of heap to use, in MB. Default is 1000.
#export HADOOP_HEAPSIZE=
#export HADOOP_NAMENODE_INIT_HEAPSIZE=""
# Extra Java runtime options. Empty by default.
export HADOOP_OPTS="$HADOOP_OPTS -Djava.net.preferIPv4Stack=true"
# Command specific options appended to HADOOP_OPTS when specified
export HADOOP_NAMENODE_OPTS="-Dhadoop.security.logger=${HADOOP_SECURITY_LOGGER:-INFO,RFAS} -Dhdfs.audit.logger=${HDFS_AUDIT_LOGGER:-INFO,NullAppender} $HADOOP_NAMENODE_OPTS"
export HADOOP_DATANODE_OPTS="-Dhadoop.security.logger=ERROR,RFAS $HADOOP_DATANODE_OPTS"
export HADOOP_SECONDARYNAMENODE_OPTS="-Dhadoop.security.logger=${HADOOP_SECURITY_LOGGER:-INFO,RFAS} -Dhdfs.audit.logger=${HDFS_AUDIT_LOGGER:-INFO,NullAppender} $HADOOP_SECONDARYNAMENODE_OPTS"
export HADOOP_NFS3_OPTS="$HADOOP_NFS3_OPTS"
export HADOOP_PORTMAP_OPTS="-Xmx512m $HADOOP_PORTMAP_OPTS"
# The following applies to multiple commands (fs, dfs, fsck, distcp etc)
export HADOOP_CLIENT_OPTS="-Xmx512m $HADOOP_CLIENT_OPTS"
#HADOOP_JAVA_PLATFORM_OPTS="-XX:-UsePerfData $HADOOP_JAVA_PLATFORM_OPTS"
# On secure datanodes, user to run the datanode as after dropping privileges.
# This **MUST** be uncommented to enable secure HDFS if using privileged ports
# to provide authentication of data transfer protocol. This **MUST NOT** be
# defined if SASL is configured for authentication of data transfer protocol
# using non-privileged ports.
export HADOOP_SECURE_DN_USER=${HADOOP_SECURE_DN_USER}
# Where log files are stored. $HADOOP_HOME/logs by default.
#export HADOOP_LOG_DIR=${HADOOP_LOG_DIR}/$USER
# Where log files are stored in the secure data environment.
export HADOOP_SECURE_DN_LOG_DIR=${HADOOP_LOG_DIR}/${HADOOP_HDFS_USER}
###
# HDFS Mover specific parameters
###
# Specify the JVM options to be used when starting the HDFS Mover.
# These options will be appended to the options specified as HADOOP_OPTS
# and therefore may override any similar flags set in HADOOP_OPTS
#
# export HADOOP_MOVER_OPTS=""
###
# Advanced Users Only!
###
# The directory where pid files are stored. /tmp by default.
# NOTE: this should be set to a directory that can only be written to by
# the user that will run the hadoop daemons. Otherwise there is the
# potential for a symlink attack.
export HADOOP_PID_DIR=${HADOOP_PID_DIR}
export HADOOP_SECURE_DN_PID_DIR=${HADOOP_PID_DIR}
# A string representing this instance of hadoop. $USER by default.
export HADOOP_IDENT_STRING=$USER
GenomicsDB-1.5.3/.github/resources/hadoop/hdfs-site.xml 0000664 0000000 0000000 00000000524 14600153730 0022726 0 ustar 00root root 0000000 0000000
dfs.data.dirfile:///opt/volume/datanodedfs.name.dirfile:///opt/volume/namenode
GenomicsDB-1.5.3/.github/scripts/ 0000775 0000000 0000000 00000000000 14600153730 0016520 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.github/scripts/cleanup_hosts.sh 0000775 0000000 0000000 00000002740 14600153730 0021731 0 ustar 00root root 0000000 0000000 #
# The MIT License (MIT)
# Copyright (c) 2021 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#!/bin/bash
# Github action build VMs seem to come with multiple 127.0.0.1 aliases in /etc/hosts
# Not sure what they do, clean them up as much as possible
sudo sed -i '/127.0.0.1/d' /etc/hosts
sudo sed -i "1 i\127.0.0.1 $(hostname)" /etc/hosts
sudo sed -i "1 i\127.0.0.1 localhost" /etc/hosts
echo "Printing /etc/hosts..."
cat /etc/hosts
echo "Printing /etc/hosts DONE"
GenomicsDB-1.5.3/.github/scripts/install_hadoop.sh 0000775 0000000 0000000 00000005425 14600153730 0022065 0 ustar 00root root 0000000 0000000 #!/bin/bash
# Install hadoop
# Installation relies on finding JAVA_HOME@/usr/java/latest as a prerequisite
INSTALL_DIR=${INSTALL_DIR:-/usr}
USER=`whoami`
HADOOP=hadoop-${HADOOP_VER:-3.3.5}
HADOOP_DIR=${INSTALL_DIR}/$HADOOP
HADOOP_ENV=${HADOOP_ENV:-$HOME/hadoop_env.sh}
JAVA_VER=${JAVA_VER:-17}
install_prereqs() {
# Java install in workflow yaml
if [[ -f /usr/java/latest ]]; then
echo "/usr/java/latest found"
sudo rm /usr/java/latest
fi
if [[ ! -z $JAVA_HOME ]]; then
sudo mkdir -p /usr/java
sudo ln -s $JAVA_HOME /usr/java/latest
else
sudo ln -s /usr/lib/jvm/java-1.${JAVA_VER}.0-openjdk-amd64/ /usr/java/latest
fi
echo "install_prereqs successful"
}
download_hadoop() {
wget -q https://archive.apache.org/dist/hadoop/common/$HADOOP/$HADOOP.tar.gz &&
tar -xzf $HADOOP.tar.gz --directory $INSTALL_DIR &&
echo "download_hadoop successful"
}
configure_passphraseless_ssh() {
sudo apt update; sudo apt -y install openssh-server
cat > sshd_config << EOF
SyslogFacility AUTHPRIV
PermitRootLogin yes
AuthorizedKeysFile .ssh/authorized_keys
PasswordAuthentication yes
ChallengeResponseAuthentication no
UsePAM yes
UseDNS no
X11Forwarding no
PrintMotd no
EOF
sudo mv sshd_config /etc/ssh/sshd_config &&
sudo systemctl restart ssh &&
rm ~/.ssh/id_rsa 2> /dev/null
ssh-keygen -q -t rsa -b 4096 -N '' -f ~/.ssh/id_rsa &&
cat ~/.ssh/id_rsa.pub | tee -a ~/.ssh/authorized_keys &&
chmod 600 ~/.ssh/authorized_keys &&
chmod 700 ~/.ssh &&
sudo chmod -c 0755 ~/ &&
echo "configure_passphraseless_ssh successful"
}
configure_hadoop() {
configure_passphraseless_ssh &&
cp -fr $GITHUB_WORKSPACE/.github/resources/hadoop/* $HADOOP_DIR/etc/hadoop &&
$HADOOP_DIR/bin/hdfs namenode -format &&
$HADOOP_DIR/sbin/start-dfs.sh &&
echo "configure_hadoop successful"
}
setup_paths() {
echo "export JAVA_HOME=/usr/java/latest" > $HADOOP_ENV
echo "export PATH=$HADOOP_DIR/bin:$PATH" >> $HADOOP_ENV
echo "export LD_LIBRARY_PATH=$HADOOP_DIR/lib:$LD_LIBRARY_PATH" >> $HADOOP_ENV
HADOOP_CP=`$HADOOP_DIR/bin/hadoop classpath --glob`
echo "export CLASSPATH=$HADOOP_CP" >> $HADOOP_ENV
echo "setup_paths successful"
}
install_hadoop() {
install_prereqs
if [[ ! -f $HADOOP_ENV ]]; then
download_hadoop &&
setup_paths &&
cp -fr $GITHUB_WORKSPACE/.github/resources/hadoop/* $HADOOP_DIR/etc/hadoop &&
mkdir -p $HADOOP_DIR/logs &&
export HADOOP_ROOT_LOGGER=ERROR,console &&
echo "install_hadoop with download successful"
fi
if [[ $? != 0 ]]; then
echo "Hadoop did not install successfully. Aborting"
exit 1
fi
source $HADOOP_ENV &&
configure_hadoop &&
echo "Install Hadoop SUCCESSFUL"
}
echo "INSTALL_DIR=$INSTALL_DIR"
install_hadoop
GenomicsDB-1.5.3/.github/scripts/install_spark.sh 0000775 0000000 0000000 00000004733 14600153730 0021734 0 ustar 00root root 0000000 0000000 #!/bin/bash
# Install spark
INSTALL_DIR=${INSTALL_DIR:-/usr}
USER=`whoami`
SPARK_VER=${SPARK_VER:-3.4.0}
SPARK=spark-$SPARK_VER-bin-hadoop${SPARK_HADOOP_VER:-3}
SPARK_DIR=${INSTALL_DIR}/$SPARK
SPARK_LOCAL_DIR="/usr/local/spark"
SPARK_ENV=${SPARK_ENV:-$HOME/spark_env.sh}
# retry logic from: https://docs.microsoft.com/en-us/azure/hdinsight/hdinsight-hadoop-script-actions-linux
MAXATTEMPTS=3
retry() {
local -r CMD="$@"
local -i ATTEMPTNUM=1
local -i RETRYINTERVAL=2
until $CMD
do
if (( ATTEMPTNUM == MAXATTEMPTS ))
then
echo "Attempt $ATTEMPTNUM failed. no more attempts left."
return 1
else
echo "Attempt $ATTEMPTNUM failed! Retrying in $RETRYINTERVAL seconds..."
sleep $(( RETRYINTERVAL ))
ATTEMPTNUM=$ATTEMPTNUM+1
fi
done
}
download_spark() {
retry wget -nv --trust-server-names "https://archive.apache.org/dist/spark/spark-$SPARK_VER/$SPARK.tgz"
sudo tar -zxf $SPARK.tgz --directory $INSTALL_DIR &&
sudo chown -R $USER:$USER $SPARK_DIR &&
sudo ln -s $INSTALL_DIR/$SPARK $SPARK_LOCAL_DIR &&
echo "download_spark successful"
}
setup_spark_env() {
echo "export SPARK_HOME=${SPARK_LOCAL_DIR}" >> $SPARK_ENV &&
echo "export PATH=${SPARK_LOCAL_DIR}/bin:${SPARK_LOCAL_DIR}/sbin:$PATH" >> $SPARK_ENV &&
echo "export CLASSPATH=$CLASSPATH" >> $SPARK_ENV &&
source $SPARK_ENV
}
configure_spark() {
echo "export SPARK_HOME=${SPARK_LOCAL_DIR}" >> $SPARK_ENV &&
echo "export PATH=${SPARK_LOCAL_DIR}/bin:${SPARK_LOCAL_DIR}/sbin:$PATH" >> $SPARK_ENV &&
echo "export CLASSPATH=$CLASSPATH" >> $SPARK_ENV &&
source $SPARK_ENV &&
sudo echo "SPARK_MASTER_HOST=127.0.0.1" > ${SPARK_LOCAL_DIR}/conf/spark-env.sh &&
sudo echo "SPARK_LOCAL_IP=127.0.0.1" >> ${SPARK_LOCAL_DIR}/conf/spark-env.sh &&
sudo echo "localhost" > ${SPARK_LOCAL_DIR}/conf/slaves &&
sudo cp ${SPARK_LOCAL_DIR}/conf/log4j2.properties.template ${SPARK_LOCAL_DIR}/conf/log4j2.properties &&
echo "configure_spark successful"
}
install_spark() {
if [[ ! -f ${SPARK_DIR}/conf/slaves ]]; then
echo "Installing Spark..."
download_spark &&
configure_spark &&
echo "Install Spark successful"
else
echo "Found cached Spark install"
fi
}
install_spark &&
if [[ ! -L ${SPARK_LOCAL_DIR} ]]; then sudo ln -s $INSTALL_DIR/$SPARK $SPARK_LOCAL_DIR; fi &&
setup_spark_env &&
${SPARK_LOCAL_DIR}/sbin/stop-master.sh &&
${SPARK_LOCAL_DIR}/sbin/start-master.sh &&
echo "Started spark"
GenomicsDB-1.5.3/.github/scripts/tag_for_docker_release.sh 0000775 0000000 0000000 00000001262 14600153730 0023530 0 ustar 00root root 0000000 0000000 #!/bin/bash
# This script is meant to be run from develop or master to add a version+commit hash tag.
# The tag will trigger the docker release workflow on Github Actions
REPO_ROOT=$(git rev-parse --show-toplevel)
CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
if [[ "$CURRENT_BRANCH" != "develop" && "$CURRENT_BRANCH" != "master" ]]; then
echo "Release should be run from develop or master branch!"
exit 1
fi
VERSION=$(grep "GenomicsDB release version" $REPO_ROOT/CMakeLists.txt | cut -d '"' -f 2)
GIT_COMMIT_HASH=$(git log -1 --format=%h)
TAG=v${VERSION}-${GIT_COMMIT_HASH}
echo "Adding tag: $TAG"
git tag -am "Tagging for docker release $TAG" $TAG
git push origin $TAG
GenomicsDB-1.5.3/.github/scripts/test_hdfs_htslib_support.sh 0000775 0000000 0000000 00000003764 14600153730 0024215 0 ustar 00root root 0000000 0000000 #
# The MIT License (MIT)
# Copyright (c) 2020 Omics Data Automation, Inc.
# Copyright (c) 2023 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#!/bin/bash
set -e
# VCFs are copied into hdfs path
# Name Node is $1 - optional
# hdfs path is $2 - optional
NAME_NODE=${1:-"hdfs://localhost:9000"}
HDFS_PATH=${2:-"/home/hadoop/input/vcfs"}
VCF_DIRS=$GITHUB_WORKSPACE/tests/inputs/vcfs
hdfs dfs -mkdir -p $NAME_NODE$HDFS_PATH
hdfs dfs -copyFromLocal $VCF_DIRS/t0.vcf.gz $NAME_NODE$HDFS_PATH
hdfs dfs -copyFromLocal $VCF_DIRS/t0.vcf.gz.tbi $NAME_NODE$HDFS_PATH
hdfs dfs -copyFromLocal $VCF_DIRS/t1.vcf.gz $NAME_NODE$HDFS_PATH
hdfs dfs -copyFromLocal $VCF_DIRS/t1.vcf.gz.tbi $NAME_NODE$HDFS_PATH
hdfs dfs -copyFromLocal $VCF_DIRS/t2.vcf.gz $NAME_NODE$HDFS_PATH
hdfs dfs -copyFromLocal $VCF_DIRS/t2.vcf.gz.tbi $NAME_NODE$HDFS_PATH
echo "$GITHUB_WORKSPACE/tests/test_hfile_plugin.sh $NAME_NODE$HDFS_PATH $CMAKE_INSTALL_PREFIX"
$GITHUB_WORKSPACE/tests/test_hfile_plugin.sh $NAME_NODE$HDFS_PATH $CMAKE_INSTALL_PREFIX
GenomicsDB-1.5.3/.github/workflows/ 0000775 0000000 0000000 00000000000 14600153730 0017066 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/.github/workflows/basic.yml 0000664 0000000 0000000 00000012714 14600153730 0020677 0 ustar 00root root 0000000 0000000 name: build
on:
push:
paths-ignore:
- '**/*.md'
- '**/*.rst'
pull_request:
paths-ignore:
- '**/*.md'
- '**/*.rst'
env:
PREREQS_ENV: ${{github.workspace}}/prereqs.sh
SPARK_ENV: ${{github.workspace}}/spark_env.sh
HADOOP_ENV: ${{github.workspace}}/hadoop_env.sh
PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs
PROTOBUF_VERSION: 3.21.7
CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install
GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build
GENOMICSDB_RELEASE_VERSION: x.y.z.test
HADOOP_VER: 3.3.5
SPARK_VER: 3.4.0
SPARK_HADOOP_VER: 3
jobs:
build:
strategy:
fail-fast: false
matrix:
os: [ubuntu-20.04,ubuntu-22.04,macos-12]
type: [basic]
java: [17]
include:
- os: ubuntu-22.04
type: hdfs
java: 17
env:
OS_TYPE: ${{matrix.os}}
JAVA_VER: ${{matrix.java}}
runs-on: ${{matrix.os}}
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: 3.9
cache: 'pip'
- uses: actions/setup-java@v3
with:
java-version: ${{matrix.java}}
distribution: temurin
java-package: jdk
cache: maven
- name: Cache built prerequisites
uses: actions/cache@v3
with:
path: |
${{env.PREREQS_INSTALL_DIR}}
~/awssdk-install
~/gcssdk-install
~/protobuf-install/${{env.PROTOBUF_VERSION}}
key: ${{matrix.os}}-cache-prereqs-${{env.PROTOBUF_VERSION}}-v1
- name: Cache Distributed FileSystems
if: matrix.type == 'hdfs'
uses: actions/cache@v3
with:
path: ${{runner.workspace}}/hadoop-${{env.HADOOP_VER}}
key: ${{matrix.os}}-dfs-${{env.HADOOP_VER}}
- name: Install Prerequisites
shell: bash
working-directory: ${{github.workspace}}/scripts/prereqs
run: |
$GITHUB_WORKSPACE/.github/scripts/cleanup_hosts.sh
if [[ ${{matrix.os}} == macos* ]]; then
echo "Installing Prerequistes for MacOS..."
INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh
else
echo "Install Prerequisites for Linux.."
sudo INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh
fi
echo "cat prereqs env..."
cat $PREREQS_ENV
echo "cat prereqs env DONE"
- name: Install spark and hadoop dependencies
if: matrix.type == 'hdfs'
shell: bash
working-directory: ${{github.workspace}}
run: |
source $GITHUB_WORKSPACE/.github/scripts/install_hadoop.sh
# Spark needs JAVA_HOME to be the jdk path
JAVA_HOME==$(dirname $(dirname $(readlink -f $(which javac)))) SPARK_ENV=$SPARK_ENV source $GITHUB_WORKSPACE/.github/scripts/install_spark.sh
env:
INSTALL_DIR: ${{runner.workspace}}
- name: Create Build Directory
shell: bash
run: mkdir -p $GENOMICSDB_BUILD_DIR
- name: Configure CMake Build
shell: bash
working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
run: |
source $PREREQS_ENV
# java tests take a very long time to run on MacOS, so limit running the tests to PRs and master/develop branches
BRANCH=${GITHUB_REF##*/}
if [[ ${{matrix.os}} != macos* || ${GITHUB_REF##*/} == master || ${GITHUB_REF##*/} == develop || $GITHUB_BASE_REF == master || $GITHUB_BASE_REF == develop ]]; then
echo "cmake BUILD_JAVA set to 1"
JAVA_BUILD_ARGS="-DBUILD_JAVA=1"
fi
if [[ ${{matrix.type}} == 'hdfs' ]]; then
HDFS_BUILD_ARGS="-DUSE_HDFS=1"
fi
cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Coverage -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \
-DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR -DGENOMICSDB_PROTOBUF_VERSION=$PROTOBUF_VERSION \
-DGENOMICSDB_RELEASE_VERSION=$GENOMICSDB_RELEASE_VERSION $JAVA_BUILD_ARGS $HDFS_BUILD_ARGS
- name: Build
working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
shell: bash
run: |
source $PREREQS_ENV
make -j4
make install
- name: Test
shell: bash
working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
if: matrix.type == 'basic'
run: |
python -m pip install --upgrade pip
python -m pip install jsondiff
make test ARGS=-V
- name: Test - Distributed FileSystems
if: matrix.type == 'hdfs'
shell: bash
working-directory: ${{github.workspace}}
run: |
python -m pip install --upgrade pip
python -m pip install jsondiff
source $SPARK_ENV
python tests/run_spark_hdfs.py $GENOMICSDB_BUILD_DIR $CMAKE_INSTALL_PREFIX local hdfs://localhost:9000/ client $GENOMICSDB_RELEASE_VERSION $GITHUB_WORKSPACE/tests "" Coverage
$GITHUB_WORKSPACE/.github/scripts/test_hdfs_htslib_support.sh
- name: Coverage
shell: bash
working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
run: |
lcov --directory . --capture --output-file coverage.info
lcov --remove coverage.info '/opt*' '/usr*' '*/dependencies/*' '*/src/test*' '*.pb.h' '*.pb.cc' '*/protobuf-install/*' '*/awssdk-install/*' '*/gcssdk-install/*' 'v1/*' '/Library/*' -o coverage.info
- name: Upload Coverage to CodeCov
uses: codecov/codecov-action@v3
with:
files: build/coverage.info, build/target/jacoco-reports/jacoco-ut/jacoco.xml, build/target/jacoco-reports/jacoco-ci/jacoco-ci.xml
verbose: true
GenomicsDB-1.5.3/.github/workflows/codeql.yml 0000664 0000000 0000000 00000006671 14600153730 0021072 0 ustar 00root root 0000000 0000000 # For most projects, this workflow file will not need changing; you simply need
# to commit it to your repository.
#
# You may wish to alter this file to override the set of languages analyzed,
# or to provide custom queries or build logic.
#
# ******** NOTE ********
# We have attempted to detect the languages in your repository. Please check
# the `language` matrix defined below to confirm you have the correct set of
# supported CodeQL languages.
#
name: "CodeQL"
on:
push:
branches: [ master, develop ]
paths:
- '**/CMakeLists.txt'
- 'pom.xml'
- 'src/main/**'
- 'src/resources/**'
- '.github/resources/codeql-config.yml'
- '.github/workflows/codeql.yml'
pull_request:
branches: [ master, develop ]
paths:
- '**/CMakeLists.txt'
- 'pom.xml'
- 'src/main/**'
- 'src/resources/**'
- '.github/resources/codeql-config.yml'
- '.github/workflows/codeql.yml'
env:
PREREQS_ENV: ${{github.workspace}}/prereqs.sh
PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs
CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install
GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build
jobs:
analyze:
name: Analyze
runs-on: ubuntu-20.04
permissions:
actions: read
contents: read
security-events: write
strategy:
fail-fast: false
# CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
# Learn more about CodeQL language support at https://git.io/codeql-language-support
steps:
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-package: jdk
java-version: '17'
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v2
with:
config-file: ./.github/resources/codeql-config.yml
languages: cpp, java
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.
# queries: ./path/to/local/query, your-org/your-repo/queries@main
- name: Cache built prerequisites for ubuntu
uses: actions/cache@v3
with:
path: |
${{env.PREREQS_INSTALL_DIR}}
~/.m2/repository
~/awssdk-install
~/gcssdk-install
~/protobuf-install
key: ubuntu-codeql-cache-prereqs-v1
- name: Build GenomicsDB
shell: bash
run: |
$GITHUB_WORKSPACE/.github/scripts/cleanup_hosts.sh
echo "Install Prerequisites for Linux.."
pushd $GITHUB_WORKSPACE/scripts/prereqs
sudo INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh
popd
echo "Install prerequisites for Linux DONE"
source $PREREQS_ENV
cmake $GITHUB_WORKSPACE -DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR -DBUILD_JAVA=1 -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX
make -j4
make install
rm -fr dependencies/ src/test/ test/
# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
# If this step fails, then you should remove it and run the build manually (see below)
# - name: Autobuild
# uses: github/codeql-action/autobuild@v1
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
GenomicsDB-1.5.3/.github/workflows/docker.yml 0000664 0000000 0000000 00000003314 14600153730 0021061 0 ustar 00root root 0000000 0000000 # from: https://docs.github.com/en/actions/publishing-packages/publishing-docker-images
name: Create and publish a Docker image
on:
push:
paths-ignore:
- '**/*.md'
- '**/*.rst'
branches:
- develop
tags:
- v*
pull_request:
paths-ignore:
- '**/*.md'
- '**/*.rst'
env:
REGISTRY: ghcr.io
IMAGE_NAME: ${{ github.repository }}
jobs:
build-and-push-image:
runs-on: ubuntu-latest
permissions:
contents: read
packages: write
steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Log in to the Container registry
uses: docker/login-action@v2
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@v4
with:
images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
- name: Build and export to Docker
uses: docker/build-push-action@v4
with:
context: .
build-args: os=ubuntu:24.04
load: true
tags: ghcr.io/genomicsdb/genomicsdb:test
- name: Test docker image
run: |
docker run --rm -v ${{github.workspace}}/tests:/opt/tests --entrypoint /opt/tests/docker_test.sh ghcr.io/genomicsdb/genomicsdb:test
- name: Build and push to ghcr.io
if: github.event_name != 'pull_request'
uses: docker/build-push-action@v4
with:
context: .
build-args: os=ubuntu:24.04
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
GenomicsDB-1.5.3/.github/workflows/release.yml 0000664 0000000 0000000 00000005653 14600153730 0021242 0 ustar 00root root 0000000 0000000 name: Release
on:
push:
tags:
- v*
env:
PREREQS_ENV: ${{github.workspace}}/prereqs.sh
PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs
PROTOBUF_VERSION: 3.19.4
CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install
GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build
BUILD_DISTRIBUTABLE_LIBRARY: true
jobs:
build-and-push-mac-dylib:
runs-on: macos-12
outputs:
tag_message: ${{env.TAG_MESSAGE}}
permissions:
contents: read
packages: write
steps:
- name: Checkout repository
uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-package: jdk
java-version: '17'
- name: Set version number
run: echo VERSION_NUMBER=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
- name: Set tag messsage
run: |
git fetch --tags --force
echo "TAG_MESSAGE=$(git tag -l --sort=-taggerdate --format='%(contents)' $(git describe --tags $(git branch --show-current) ))" >> $GITHUB_ENV
- name: Install Prerequisites
shell: bash
working-directory: ${{github.workspace}}/scripts/prereqs
run: |
echo "Installing Prerequistes for MacOS..."
export INSTALL_PREFIX=$PREREQS_INSTALL_DIR
BUILD_DISTRIBUTABLE_LIBRARY=true ./install_prereqs.sh
- name: Build GenomicsDB distributable
shell: bash
run: |
echo "Building GenomicsDB for MacOS..."
export INSTALL_PREFIX=$PREREQS_INSTALL_DIR
mkdir -p $GENOMICSDB_BUILD_DIR
source $PREREQS_ENV
cmake $GITHUB_WORKSPACE \
-DCMAKE_OSX_ARCHITECTURES="arm64;x86_64" \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \
-DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR \
-DGENOMICSDB_PROTOBUF_VERSION=$PROTOBUF_VERSION \
-DGENOMICSDB_RELEASE_VERSION=${VERSION_NUMBER} \
-DBUILD_JAVA=1 -DUSE_HDFS=0 -DBUILD_DISTRIBUTABLE_LIBRARY=1
make -j4
make install
cp $CMAKE_INSTALL_PREFIX/lib/libtiledbgenomicsdb.dylib .
- name: Archive libraries as artifact
uses: actions/upload-artifact@v3
with:
name: libtiledbgenomicsdb.dylib.${{ github.ref_name }}
path: libtiledbgenomicsdb.dylib
release-jar:
needs: [build-and-push-mac-dylib]
uses: ./.github/workflows/release_jar.yml
with:
dylib_artifact: libtiledbgenomicsdb.dylib.${{ github.ref_name }}
test:
needs: [build-and-push-mac-dylib, release-jar]
uses: ./.github/workflows/release_test.yml
with:
release_artifact: release.${{ github.ref_name }}
tag_message: ${{ needs.build-and-push-mac-dylib.outputs.tag_message }}
publish:
needs: [test]
uses: ./.github/workflows/release_publish.yml
with:
release_artifact: release.${{ github.ref_name }}
secrets: inherit
GenomicsDB-1.5.3/.github/workflows/release_jar.yml 0000664 0000000 0000000 00000004567 14600153730 0022101 0 ustar 00root root 0000000 0000000 name: Build release jar
on:
workflow_call:
inputs:
dylib_artifact:
required: true
type: string
jobs:
build-and-push-jar:
runs-on: ubuntu-latest
permissions:
contents: read
packages: write
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
submodules: true # cmake does this for us...but need to patch htslib before calling cmake
- name: Set version number
run: echo VERSION_NUMBER=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
- name: Download dylib
uses: actions/download-artifact@v3
with:
name: ${{ inputs.dylib_artifact }}
- name: Build Centos 6 and create release jar
uses: docker/build-push-action@v4
with:
context: .
file: Dockerfile.release
build-args: |
GENOMICSDB_RELEASE_VERSION=${{ env.VERSION_NUMBER }}
MAC_DYLIB_PATH=/opt/libtiledbgenomicsdb.dylib
USE_HDFS=true
load: true
tags: ghcr.io/genomicsdb/genomicsdb:release
- name: Get artifacts from docker image
shell: bash
run: |
docker create -it --name genomicsdb ghcr.io/genomicsdb/genomicsdb:release bash
docker cp genomicsdb:/build/GenomicsDB/build/src/main/libtiledbgenomicsdb.so .
docker cp genomicsdb:/build/GenomicsDB/build/target/genomicsdb-${VERSION_NUMBER}.jar .
docker cp genomicsdb:/build/GenomicsDB/build/target/genomicsdb-${VERSION_NUMBER}-allinone-spark.jar .
docker cp genomicsdb:/build/GenomicsDB/build/target/genomicsdb-${VERSION_NUMBER}-sources.jar .
docker cp genomicsdb:/build/GenomicsDB/build/target/genomicsdb-${VERSION_NUMBER}-javadoc.jar .
docker cp genomicsdb:/build/GenomicsDB/pom.xml genomicsdb-${VERSION_NUMBER}.pom
docker cp genomicsdb:/build/GenomicsDB/build/target/genomicsdb-spark-${VERSION_NUMBER}.jar .
sed -i.bak 's/${genomicsdb.version}/'"${VERSION_NUMBER}"'/' genomicsdb-${VERSION_NUMBER}.pom
- name: Archive libraries as artifact
uses: actions/upload-artifact@v3
with:
name: release.${{ github.ref_name }}
path: |
libtiledbgenomicsdb.*
genomicsdb-${{ env.VERSION_NUMBER }}*.jar
genomicsdb-spark-${{ env.VERSION_NUMBER }}*.jar
genomicsdb-${{ env.VERSION_NUMBER }}.pom
GenomicsDB-1.5.3/.github/workflows/release_publish.yml 0000664 0000000 0000000 00000007435 14600153730 0022770 0 ustar 00root root 0000000 0000000 name: Publish release jar
on:
workflow_call:
inputs:
release_artifact:
required: true
type: string
secrets:
MAVEN_GPG_PASSPHRASE:
required: true
MAVEN_GPG_PRIVATE_KEY:
required: true
OSSRH_USERNAME:
required: true
OSSRH_PASSWORD:
required: true
jobs:
publish-jar:
runs-on: ubuntu-latest
permissions:
contents: read
packages: write
steps:
- name: Set version number
run: echo VERSION_NUMBER=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
- uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-version: '17'
server-id: ossrh
server-username: OSSRH_USERNAME
server-password: OSSRH_PASSWORD
gpg-private-key: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}
gpg-passphrase: MAVEN_GPG_PASSPHRASE
- name: Download release artifacts
uses: actions/download-artifact@v3
with:
name: ${{ inputs.release_artifact }}
- name: Deploy Maven Central
shell: bash
run: |
sudo apt install -y xmlstarlet
if [[ ${VERSION_NUMBER} = *SNAPSHOT ]]; then
URL=`xmlstarlet sel -t -m "//_:project" -v _:distributionManagement/_:snapshotRepository/_:url genomicsdb-${VERSION_NUMBER}.pom`
REPO_ID=`xmlstarlet sel -t -m "//_:project" -v _:distributionManagement/_:snapshotRepository/_:id genomicsdb-${VERSION_NUMBER}.pom`
else
URL=`xmlstarlet sel -t -m "//_:project" -v _:distributionManagement/_:repository/_:url genomicsdb-${VERSION_NUMBER}.pom`
REPO_ID=`xmlstarlet sel -t -m "//_:project" -v _:distributionManagement/_:repository/_:id genomicsdb-${VERSION_NUMBER}.pom`
fi
echo "Deploying jars..."
# main jar
mvn gpg:sign-and-deploy-file -Durl=$URL -Dfile=genomicsdb-${VERSION_NUMBER}.jar \
-DgroupId=org.genomicsdb -DartifactId=genomicsdb -Dversion=${VERSION_NUMBER} \
-Dpackaging=jar -DpomFile=genomicsdb-${VERSION_NUMBER}.pom -DrepositoryId=$REPO_ID \
-Djavadoc=genomicsdb-${VERSION_NUMBER}-javadoc.jar \
-Dsources=genomicsdb-${VERSION_NUMBER}-sources.jar \
-Dfiles=genomicsdb-${VERSION_NUMBER}-allinone-spark.jar -Dtypes=jar -Dclassifiers=allinone
# spark jar
mvn gpg:sign-and-deploy-file -Durl=$URL -Dfile=genomicsdb-spark-${VERSION_NUMBER}.jar \
-DgroupId=org.genomicsdb -DartifactId=genomicsdb-spark -Dversion=${VERSION_NUMBER} \
-Dpackaging=jar -DpomFile=genomicsdb-${VERSION_NUMBER}.pom -DrepositoryId=$REPO_ID \
-Djavadoc=genomicsdb-${VERSION_NUMBER}-javadoc.jar \
-Dsources=genomicsdb-${VERSION_NUMBER}-sources.jar
echo "Deploying jars DONE"
# publish
if [[ ${VERSION_NUMBER} != *SNAPSHOT ]]; then
echo "Gather Sonatype staging repository ID..."
stagingRepoId=$(mvn nexus-staging:rc-list -DnexusUrl=https://oss.sonatype.org/ -DserverId=ossrh -f genomicsdb-${VERSION_NUMBER}.pom| awk '/orggenomicsdb/ {print $2}')
echo "Staging Repository ID: $stagingRepoId"
echo "Releasing staged repository..."
mvn nexus-staging:rc-close -DserverId=ossrh -DnexusUrl=https://oss.sonatype.org/ -DstagingRepositoryId=$stagingRepoId -f genomicsdb-${VERSION_NUMBER}.pom
mvn nexus-staging:rc-release -DserverId=ossrh -DnexusUrl=https://oss.sonatype.org/ -DstagingRepositoryId=$stagingRepoId -f genomicsdb-${VERSION_NUMBER}.pom
echo "Releasing staged repository DONE"
fi
env:
OSSRH_USERNAME: ${{ secrets.OSSRH_USERNAME }}
OSSRH_PASSWORD: ${{ secrets.OSSRH_PASSWORD }}
MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
GenomicsDB-1.5.3/.github/workflows/release_test.yml 0000664 0000000 0000000 00000004122 14600153730 0022267 0 ustar 00root root 0000000 0000000 name: Test release jar
on:
workflow_call:
inputs:
release_artifact:
required: true
type: string
tag_message:
required: false
type: string
jobs:
test-jar:
strategy:
fail-fast: true
matrix:
os: [ubuntu-latest,macos-12]
runs-on: ${{matrix.os}}
permissions:
contents: read
packages: write
steps:
- name: Checkout TestGenomicsDBJar
uses: actions/checkout@v3
with:
repository: GenomicsDB/TestGenomicsDBJar
ref: master
- name: Set version number
run: |
echo ${{github.ref_name}}
echo VERSION_NUMBER=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
echo GENOMICSDB_VERSION=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
echo GENOMICSDB_MIN_TAG=v1.5.2-SNAPSHOT >> $GITHUB_ENV
- uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-version: '17'
- name: Download release artifacts
uses: actions/download-artifact@v3
with:
name: ${{ inputs.release_artifact }}
- name: Run smoke test
shell: bash
run: |
if [ $(uname) == "Darwin" ]; then sw_vers; fi
mvn install:install-file -Dfile=genomicsdb-${VERSION_NUMBER}.jar \
-DgroupId=org.genomicsdb -DartifactId=genomicsdb -Dversion=${VERSION_NUMBER} \
-Dpackaging=jar -DpomFile=genomicsdb-${VERSION_NUMBER}.pom
GENOMICSDB_TAG=${GITHUB_REF_NAME} ./test_genomicsdbjar.sh
- name: Run compatibility test
shell: bash
run: GENOMICSDB_TAG=${GENOMICSDB_MIN_TAG} ./test_genomicsdbjar.sh
- name: Checkout GATK
if: ${{ !contains(inputs.tag_message,'skip-gatk-it') }}
uses: actions/checkout@v3
with:
repository: broadinstitute/gatk
lfs: 'true'
- name: Try GATK integration test
if: ${{ !contains(inputs.tag_message,'skip-gatk-it') }}
shell: bash
run: |
./gradlew installDist -Dgenomicsdb.version=${VERSION_NUMBER}
./gradlew test --tests *GenomicsDB*
GenomicsDB-1.5.3/.gitignore 0000664 0000000 0000000 00000001677 14600153730 0015474 0 ustar 00root root 0000000 0000000 *.swp
*.o
*.a
*.so
*.d
test_inputs
my_workspace*
.directory
examples/bin/*
examples/obj/*
*temp*
.project
.cproject
bin/*
*.gcno
*.gcda
tests/coverage.info
*.class
*.jar
*.iml
.idea/*
/target/
.tmp_loader.json
build/
src/main/java/com/intel/genomicsdb/model/GenomicsDBCallsetsMapProto.java
src/main/java/com/intel/genomicsdb/model/GenomicsDBExportConfiguration.java
src/main/java/com/intel/genomicsdb/model/GenomicsDBImportConfiguration.java
src/main/java/com/intel/genomicsdb/model/GenomicsDBVidMapProto.java
src/main/java/com/intel/genomicsdb/model/Coordinates.java
src/main/java/com/intel/genomicsdb/GenomicsDBCallsetsMapProto.java
src/main/java/com/intel/genomicsdb/GenomicsDBExportConfiguration.java
src/main/java/com/intel/genomicsdb/GenomicsDBImportConfiguration.java
src/main/java/com/intel/genomicsdb/GenomicsDBVidMapProto.java
#python
*.pyc
#emacs
*~
\#*\#
.\#*
TAGS
#Xcode
.DS_Store
#vs-code
.vscode/*
*/env/*
docs/_build/
env/*
docs/doxydocs
GenomicsDB-1.5.3/.gitmodules 0000664 0000000 0000000 00000001053 14600153730 0015645 0 ustar 00root root 0000000 0000000 [submodule "dependencies/htslib"]
path = dependencies/htslib
url = https://github.com/GenomicsDB/htslib.git
[submodule "dependencies/TileDB"]
path = dependencies/TileDB
url = https://github.com/OmicsDataAutomation/TileDB.git
[submodule "dependencies/RapidJSON"]
path = dependencies/RapidJSON
url = https://github.com/miloyip/rapidjson.git
[submodule "src/test/cpp/Catch2"]
path = src/test/cpp/Catch2
url = https://github.com/catchorg/Catch2
[submodule "dependencies/spdlog"]
path = dependencies/spdlog
url = https://github.com/gabime/spdlog.git
GenomicsDB-1.5.3/.readthedocs.yml 0000664 0000000 0000000 00000002030 14600153730 0016552 0 ustar 00root root 0000000 0000000 # .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
# Required
version: 2
# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: docs/conf.py
build:
os: ubuntu-20.04
tools:
python: "3.10"
apt_packages:
- protobuf-compiler
jobs:
pre_build:
- cd docs && doxygen
- wget -c https://github.com/pseudomuto/protoc-gen-doc/releases/download/v1.5.1/protoc-gen-doc_1.5.1_linux_amd64.tar.gz -O - | tar -xz
- mkdir -p docs/protodoc
- cd src/resources && protoc --plugin=protoc-gen-doc=../../protoc-gen-doc --doc_out=../../docs/protodoc --doc_opt=../../docs/protodoc.tmpl,proto.md *proto
- cd dependencies && git clone --no-single-branch --depth 50 https://github.com/GenomicsDB/GenomicsDB-Python.git GenomicsDB-Python
- mv dependencies/GenomicsDB-Python/genomicsdb dependencies/GenomicsDB-Python/genomicsdb_data
formats:
- pdf
python:
install:
- requirements: docs/requirements.txt
GenomicsDB-1.5.3/CMakeLists.txt 0000664 0000000 0000000 00000066107 14600153730 0016243 0 ustar 00root root 0000000 0000000 #
# CMakeLists.txt
#
# The MIT License
#
# Copyright (c) 2019-2023 Omics Data Automation, Inc.
# Copyright (c) 2023 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
cmake_minimum_required(VERSION 3.17)
#GIT_COMMIT_HASH derived from git tag to be used as part of GENOMICSDB_VERSION
execute_process(
COMMAND git log -1 --format=%h
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
OUTPUT_VARIABLE GIT_COMMIT_HASH
OUTPUT_STRIP_TRAILING_WHITESPACE
)
#Build versions
set(GENOMICSDB_RELEASE_VERSION "1.5.3-SNAPSHOT" CACHE STRING "GenomicsDB release version") #used in Maven builds
string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" GENOMICSDB_BASE_VERSION "${GENOMICSDB_RELEASE_VERSION}")
#GIT_COMMIT_HASH derived from git tag to be used as part of GENOMICSDB_VERSION
execute_process(
COMMAND git log -1 --format=%h
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
OUTPUT_VARIABLE GIT_COMMIT_HASH
OUTPUT_STRIP_TRAILING_WHITESPACE
)
set(GENOMICSDB_VERSION "${GENOMICSDB_RELEASE_VERSION}-${GIT_COMMIT_HASH}" CACHE STRING "GenomicsDB full version string")
message(STATUS "GenomicsDB version=${GENOMICSDB_BASE_VERSION} full_version=${GENOMICSDB_RELEASE_VERSION}-${GIT_COMMIT_HASH}")
#project
project(GenomicsDB DESCRIPTION "High performance data storage for import/query/transform of variants" VERSION ${GENOMICSDB_BASE_VERSION})
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake/Modules")
if (NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU")
message(FATAL_ERROR CMAKE_CXX_COMPILER_ID " Compiler not yet supported. Exiting.")
endif()
#External dependencies. Can be overridden to point to custom locations
set(HTSLIB_SOURCE_DIR "${CMAKE_SOURCE_DIR}/dependencies/htslib" CACHE PATH "Path to htslib source directory")
set(TILEDB_SOURCE_DIR "${CMAKE_SOURCE_DIR}/dependencies/TileDB" CACHE PATH "Path to TileDB source directory")
set(RAPIDJSON_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/dependencies/RapidJSON/include" CACHE PATH "Path to RapidJSON include directory")
set(SPDLOG_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/dependencies/spdlog/include" CACHE PATH "Path to SpdLog include directory")
#The fmt headers are in dependencies/spdlog/include/spdlog/fmt/bundled - source files will include "fmt/bundled/format.h"
set(FMT_ROOT_DIR "${SPDLOG_INCLUDE_DIR}" CACHE PATH "Path to fmt library")
set(USING_FMT_BUNDLED_WITH_SPDLOG True CACHE BOOL "Disable if using fmt library that's not bundled with spdlog")
#Build parameters/options
option(BUILD_DISTRIBUTABLE_LIBRARY "Build the GenomicsDB library with minimal runtime dependencies")
option(BUILD_JAVA "Build Java/JNI interface for combined VCF records")
option(BUILD_FOR_PYTHON "Build GenomicsDB library with minimal runtime, no jvm/openssl/curl dependencies and python protobuf bindings")
option(BUILD_FOR_GO "Build GenomicsDB library with minimal runtime, no jvm/openssl/curl dependencies and go protobuf bindings")
option(BUILD_FOR_R "Build GenomicsDB library with minimal runtime, no jvm/openssl/curl dependencies and R protobuf bindings")
option(DISABLE_MPI "Disable use of any MPI compiler/libraries")
option(DISABLE_OPENMP "Disable OpenMP")
option(DISABLE_TOOLS "Disable build of tools")
set(HTSLIB_INSTALL_DIR "" CACHE PATH "Path to htslib install directory")
#Sync the GENOMICSDB_PROTOBUF_VERSION with protobuf.version in pom.xml!
set(GENOMICSDB_PROTOBUF_VERSION "3.21.7" CACHE STRING "Version of Google Protocol Buffer library")
set(PROTOBUF_ROOT_DIR "$ENV{HOME}/protobuf-install/${GENOMICSDB_PROTOBUF_VERSION}" CACHE PATH "Path to installed protobuf")
set(PROTOBUF_URL "https://github.com/protocolbuffers/protobuf/archive/v${GENOMICSDB_PROTOBUF_VERSION}.zip" CACHE STRING "URL to protobuf github release")
set(PROTOBUF_REGENERATE True CACHE BOOL "Regenerate protocol buffers C++ files")
set(GENERATE_PROTOBUF_FILES_IN_BUILD_DIR True CACHE BOOL "Generate all protobuf files in build directory")
set(USE_LIBCSV False CACHE BOOL "Enable library components that import data from csv files")
set(LIBCSV_DIR "" CACHE PATH "Path to libcsv header and library")
#Testing
option(DISABLE_TESTING "Disable testing of builds")
#Profiling
option(DO_PROFILING "Collect some stats during execution - doesn't add much overhead")
option(COUNT_NUM_CELLS_BETWEEN_TWO_CELLS_FROM_THE_SAME_ROW "Counting #cells traversed in columnar iterator")
option(PROFILE_NUM_CELLS_TO_TRAVERSE_AT_EVERY_QUERY_INTERVAL "Counting #cells traversed in columnar iterator in sliding window")
option(DO_MEMORY_PROFILING "Collect memory consumption in parts of the combine gVCF program - high overhead")
#See https://gperftools.github.io/gperftools/cpuprofile.html
option(USE_GPERFTOOLS "Collect profiling information using gperftools/profiler for analysis with pprof")
#See https://gperftools.github.io/gperftools/heapprofile.html
option(USE_GPERFTOOLS_HEAP "Collect heap profiling information using gperftools/tcmalloc for analysis with pprof")
set(GENOMICSDB_MAVEN_BUILD_DIR ${CMAKE_BINARY_DIR}/target CACHE PATH "Path to maven build directory")
set(MAVEN_QUIET False CACHE BOOL "Do not print mvn messages")
set(GPG_PASSPHRASE "" CACHE STRING "Gpg passphrase for deploying to maven")
set(IPPROOT "" CACHE PATH "Path to IPP libraries - used when intel optimized zlib is required")
set(LIBDBI_DIR "" CACHE PATH "Path to libdbi install directory")
# if no build build type is specified, default to release builds
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release CACHE STRING "GenomicsDB default set to Release" FORCE)
endif()
message(STATUS "CMAKE_BUILD_TYPE=" ${CMAKE_BUILD_TYPE})
set(USE_HDFS False CACHE BOOL "Enables HDFS support")
set(BUILD_FOR_ARCH "" CACHE STRING "Arch for which to build - values passed to -march= option for gcc")
# The DOWNLOAD_EXTRACT_TIMESTAMP option to the ExternalProject_Add() command is used to explicitly specify
# how timestamps should be handled. The default behavior is to set the timestamps of extracted contents to
# the time of extraction.
# https://cmake.org/cmake/help/latest/policy/CMP0135.html#policy:CMP0135
if(POLICY CMP0135)
cmake_policy(SET CMP0135 NEW)
endif()
# Honor visibility properties for all target types.
# https://cmake.org/cmake/help/latest/policy/CMP0063.html
if(POLICY CMP0063)
cmake_policy(SET CMP0063 NEW)
endif()
#See https://cmake.org/Wiki/CMake_RPATH_handling#Common_questions
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH True)
if(APPLE)
set(CMAKE_MACOSX_RPATH True CACHE BOOL "Set rpath on OSX")
set(CMAKE_FIND_FRAMEWORK LAST CACHE STRING "Try to find frameworks on Mac OS X last")
endif()
if(NOT DISABLE_TESTING)
enable_testing()
endif()
#Platform check modules
include(CheckIncludeFileCXX)
include(CheckCXXSymbolExists)
#Optimization flag
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND BUILD_FOR_ARCH)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${BUILD_FOR_ARCH}")
endif()
if(BUILD_FOR_PYTHON OR BUILD_FOR_GO OR BUILD_FOR_R)
set(BUILD_BINDINGS TRUE)
endif()
if(BUILD_DISTRIBUTABLE_LIBRARY OR BUILD_BINDINGS)
set(DISABLE_MPI True)
set(DISABLE_OPENMP True)
set(DISABLE_TOOLS True)
set(DISABLE_EXAMPLES True)
endif()
if (BUILD_DISTRIBUTABLE_LIBRARY AND NOT BUILD_BINDINGS)
#For the GNU compiler, link in static gcc libraries
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -static-libgcc -static-libstdc++")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++")
endif()
endif()
#Check for minimum C++11 support, but use C++17 if possible
include(CheckAndSetStdCXX2011Flag)
CHECK_AND_SET_STD_CXX_2011_FLAG(test_cpp_2011)
if(NOT test_cpp_2011)
message(FATAL_ERROR "Your compiler does not support C++ 2011, exiting")
endif()
#Check for stack-protector-strong
include(CheckAndSetStackProtectorStrong)
CHECK_AND_SET_STACK_PROTECTOR_STRONG_FLAG(test_stack_protector_strong)
if(NOT test_stack_protector_strong)
message(STATUS "Using -fstack-protector instead of -fstack-protector-strong")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fstack-protector")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fstack-protector")
endif()
#Compiler Warning Options
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result")
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -z noexecstack -z relro -z now")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -z noexecstack -z relro -z now")
elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-reorder -Wno-unused-variable -Wno-pessimizing-move -Wno-deprecated-declarations")
endif()
#MPI library/compiler etc
if(NOT DISABLE_MPI)
find_package(MPI)
if (NOT MPI_FOUND)
# see https://gitlab.kitware.com/cmake/cmake/issues/21955
# Usually happens off and on Apple, so try again explicitly
message(STATUS "Could not find MPI using find_package, trying to find MPI explicitly")
find_file(MPI_H_FILE mpi.h REQUIRED)
find_library(MPICXX_LIB_FILE NAMES mpichcxx REQUIRED)
find_library(MPICH_LIB_FILE NAMES mpich REQUIRED)
if(MPI_H_FILE AND MPICXX_LIB_FILE AND MPICH_LIB_FILE)
set(MPI_FOUND True)
cmake_path(GET MPI_H_FILE PARENT_PATH MPI_CXX_INCLUDE_PATH)
set(MPI_CXX_LIBRARIES ${MPICXX_LIB_FILE} ${MPICH_LIB_FILE})
message(STATUS "Found MPI ${MPI_H_FILE}")
else()
message(FATAL "Could not find MPI include files and libraries")
endif()
endif()
include_directories(${MPI_CXX_INCLUDE_PATH})
else()
add_definitions(-DDISABLE_MPI=1)
endif()
if(NOT DISABLE_OPENMP)
find_package(OpenMPv4)
if(NOT OPENMPV4_FOUND)
set(DISABLE_OPENMP True)
else()
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
endif()
if(DISABLE_OPENMP)
add_definitions(-DDISABLE_OPENMP=1)
endif()
add_definitions(-D_FILE_OFFSET_BITS=64) #large file support
add_definitions(-DDUPLICATE_CELL_AT_END=1) #mandatory
add_definitions(-DGENOMICSDB_VERSION=\"${GENOMICSDB_VERSION}\")
if(CMAKE_BUILD_TYPE STREQUAL "Release" AND CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 12.0)
add_definitions(-D_FORTIFY_SOURCE=2)
endif()
find_package(StringView)
if(NOT STRING_VIEW_FOUND AND NOT STRING_VIEW_EXPERIMENTAL_FOUND)
message(FATAL_ERROR "No string_view found. Use a compiler that supports std::string_view for now")
endif()
find_package(libuuid REQUIRED)
include_directories(${LIBUUID_INCLUDE_DIR})
if(BUILD_DISTRIBUTABLE_LIBRARY)
set(OPENSSL_USE_STATIC_LIBS TRUE)
endif()
#OpenSSL required by TileDB and CURL
find_package(OpenSSL REQUIRED)
find_package(CURL REQUIRED)
#RapidJSON
find_package(RapidJSON REQUIRED)
include_directories(${RAPIDJSON_INCLUDE_DIR})
#SpdLog
find_package(Spdlog REQUIRED)
include_directories(${SPDLOG_INCLUDE_DIR})
#htslib
find_package(htslib REQUIRED)
include_directories(BEFORE ${HTSLIB_INCLUDE_DIR})
#librt
find_library(LIBRT_LIBRARY rt)
#fmt library
find_package(fmt REQUIRED)
include_directories(${FMT_INCLUDE_DIR})
if(USING_FMT_BUNDLED_WITH_SPDLOG)
add_definitions(-DUSING_FMT_BUNDLED_WITH_SPDLOG)
endif()
#pgsql driver and dbi libs
#find_package(libdbi)
#if(LIBDBI_FOUND)
#include_directories(${LIBDBI_INCLUDE_DIR})
#add_definitions(-DLIBDBI)
#endif()
include(GNUInstallDirs)
#Protobuf library
find_package(ProtobufWrapper REQUIRED)
if(GENERATE_PROTOBUF_FILES_IN_BUILD_DIR)
set(PROTOBUF_JAVA_OUTPUT_DIR "${CMAKE_BINARY_DIR}/src/main/java")
else()
set(PROTOBUF_JAVA_OUTPUT_DIR "${CMAKE_SOURCE_DIR}/src/main/java")
endif()
include_directories(${PROTOBUF_INCLUDE_DIRS})
#JNI
if(BUILD_JAVA OR USE_HDFS)
if(CMAKE_CROSSCOMPILING)
set(JAVA_HOME ${TARGET_JAVA_HOME})
set(ENV{JAVA_HOME} ${TARGET_JAVA_HOME})
endif()
find_package(JNI REQUIRED)
if(CMAKE_CROSSCOMPILING)
unset(JAVA_HOME)
unset(ENV{JAVA_HOME})
endif()
if (BUILD_JAVA)
find_package(Java 17 REQUIRED)
endif()
include_directories(${JNI_INCLUDE_DIRS})
include_directories(src/main/jni/include)
include(UseJava)
endif()
#TileDB
find_package(TileDB REQUIRED)
include_directories(${TILEDB_INCLUDE_DIR})
#libcsv
if(NOT BUILD_DISTRIBUTABLE_LIBRARY AND NOT BUILD_BINDINGS)
if(USE_LIBCSV)
find_package(libcsv REQUIRED)
else()
find_package(libcsv)
endif()
endif()
if(LIBCSV_FOUND)
include_directories(${LIBCSV_INCLUDE_DIR})
set(USE_LIBCSV True)
add_definitions(-DUSE_LIBCSV)
endif()
#Collect stats
if(DO_PROFILING)
message(STATUS "Enabling stats collection")
add_definitions(-DDO_PROFILING=1)
#Collect some more stats
if(COUNT_NUM_CELLS_BETWEEN_TWO_CELLS_FROM_THE_SAME_ROW)
message(STATUS "Enabling COUNT_NUM_CELLS_BETWEEN_TWO_CELLS_FROM_THE_SAME_ROW")
add_definitions(-DCOUNT_NUM_CELLS_BETWEEN_TWO_CELLS_FROM_THE_SAME_ROW=1)
endif()
if(PROFILE_NUM_CELLS_TO_TRAVERSE_AT_EVERY_QUERY_INTERVAL)
message(STATUS "Enabling PROFILE_NUM_CELLS_TO_TRAVERSE_AT_EVERY_QUERY_INTERVAL")
add_definitions(-DPROFILE_NUM_CELLS_TO_TRAVERSE_AT_EVERY_QUERY_INTERVAL=1)
endif()
endif()
#Collect stats to use with gperf/pprof
#See https://gperftools.github.io/gperftools/cpuprofile.html
#See https://gperftools.github.io/gperftools/heapprofile.html
if(USE_GPERFTOOLS OR USE_GPERFTOOLS_HEAP)
find_package(GPerftools)
if(GPERFTOOLS_FOUND OR GPERFTOOLS_HEAP_FOUND)
message(STATUS "Enabling profiling using GPerftools")
include_directories(${GPERFTOOLS_INCLUDE_DIR})
if(USE_GPERFTOOLS)
add_definitions(-DUSE_GPERFTOOLS)
endif()
if(USE_GPERFTOOLS_HEAP)
add_definitions(-DUSE_GPERFTOOLS_HEAP)
endif()
else()
message(WARNING "GPerftools headers/library not found")
endif()
endif()
#Collect memory consumption stats while producing combined VCF records
if(DO_MEMORY_PROFILING)
message(STATUS "Enabling memory consumption profiling while producing combined VCF records")
add_definitions(-DDO_MEMORY_PROFILING=1)
endif()
#Produce verbose output
if(VERBOSE)
add_definitions(-DVERBOSE=${VERBOSE})
message(STATUS "Programs will produce output with verbosity=${VERBOSE}")
endif()
set(CMAKE_CXX_FLAGS_DEBUG "-DDEBUG -g3 -gdwarf-3")
set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3 -fvisibility=hidden")
set(CMAKE_CXX_FLAGS_COVERAGE "-DDEBUG -g3 -gdwarf-3 --coverage")
#Clean all
add_custom_target(clean-all ${CMAKE_MAKE_PROGRAM} clean)
if(TILEDB_SOURCE_DIR)
add_custom_target(clean-TileDB ${CMAKE_COMMAND} -E remove_directory ${TILEDB_DIR_IN_BUILD_DIR})
add_dependencies(clean-all clean-TileDB)
endif()
if(HTSLIB_SOURCE_DIR)
add_custom_target(clean-htslib ${CMAKE_COMMAND} -E remove_directory ${HTSLIB_DIR_IN_BUILD_DIR})
add_dependencies(clean-all clean-htslib)
endif()
#Uninstall GenomicsDB
add_custom_target(
uninstall-genomicsdb
COMMAND echo "-- Uninstalling GenomicsDB from ${CMAKE_INSTALL_PREFIX}..."
COMMAND < install_manifest.txt xargs -I % sh -c 'echo -- Uninstalling % && rm -f %' %
COMMAND echo "-- GenomicsDB is uninstalled!"
)
find_package(safestringlib)
if(SAFESTRINGLIB_FOUND)
add_definitions(-DSAFESTRINGLIB_FOUND=1)
include_directories(${SAFESTRINGLIB_INCLUDE_DIR})
endif()
include_directories (
src/main/cpp/include/genomicsdb
src/main/cpp/include/loader
src/main/cpp/include/query_operations
src/main/cpp/include/utils
src/main/cpp/include/vcf
src/main/cpp/include/config
src/main/cpp/include/api
src/test/cpp/include
)
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${PROTOBUF_LIBRARIES})
if(MPI_FOUND)
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES} ${MPI_CXX_LIBRARIES})
endif()
if(USE_HDFS)
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES} ${JAVA_JVM_LIBRARY})
endif()
if(CURL_FOUND)
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES} ${CURL_LIBRARIES})
endif()
if(SAFESTRINGLIB_FOUND)
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES} ${SAFESTRINGLIB_LIBRARY})
endif()
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES}
${OPENSSL_LIBRARIES} ${ZLIB_LIBRARIES} ${LIBUUID_LIBRARY} ${CMAKE_DL_LIBS})
if(IPPROOT AND ${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
find_package(IPP REQUIRED)
set(GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES}
${LIBIPPDC_LIBRARY} ${LIBIPPS_LIBRARY} ${LIBIPPCORE_LIBRARY})
endif()
function(build_GenomicsDB_executable_common target)
build_GenomicsDB_links(${target})
install(TARGETS ${target} RUNTIME DESTINATION bin)
endfunction()
function(build_GenomicsDB_links target)
set_property(TARGET ${target} PROPERTY POSITION_INDEPENDENT_CODE ON)
#add_executable(${target} src/${target}.cc)
target_link_libraries(${target} genomicsdb)
if(TILEDB_SOURCE_DIR)
target_link_libraries(${target} tiledb_static)
else()
target_link_libraries(${target} ${TILEDB_LIBRARY})
endif()
if(HTSLIB_SOURCE_DIR)
add_dependencies(${target} htslib)
endif()
target_link_libraries(${target} ${HTSLIB_LIBRARY})
if(LIBCSV_FOUND)
target_link_libraries(${target} ${LIBCSV_LIBRARY})
endif()
if(LIBDBI_FOUND)
target_link_libraries(${target} ${LIBPGSQL_DRIVER_LIBRARY} ${LIBDBI_DEV_LIBRARY})
endif()
if(LIBRT_LIBRARY)
target_link_libraries(${target} ${LIBRT_LIBRARY})
endif()
if(USE_GPERFTOOLS AND GPERFTOOLS_FOUND)
target_link_libraries(${target} ${GPERFTOOLS_PROFILER_LIBRARY})
endif()
if(USE_GPERFTOOLS_HEAP AND GPERFTOOLS_FOUND)
target_link_libraries(${target} ${GPERFTOOLS_HEAP_PROFILER_LIBRARY})
endif()
target_link_libraries(${target} ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES})
endfunction()
function(build_GenomicsDB_executable target)
add_executable(${target} src/${target}.cc)
build_GenomicsDB_executable_common(${target})
endfunction()
add_subdirectory(src)
include_directories(${PROTOBUF_GENERATED_CXX_HDRS_INCLUDE_DIRS})
if(NOT DISABLE_TOOLS)
add_subdirectory(tools)
endif()
if(NOT DISABLE_EXAMPLES)
add_subdirectory(example)
endif()
if(BUILD_JAVA)
set(JAVA_SCALA_SOURCES
./src/main/java/org/genomicsdb/exception/GenomicsDBException.java
./src/main/java/org/genomicsdb/importer/extensions/CallSetMapExtensions.java
./src/main/java/org/genomicsdb/importer/extensions/JsonFileExtensions.java
./src/main/java/org/genomicsdb/importer/extensions/VidMapExtensions.java
./src/main/java/org/genomicsdb/importer/model/ChromosomeInterval.java
./src/main/java/org/genomicsdb/importer/model/SampleInfo.java
./src/main/java/org/genomicsdb/importer/Constants.java
./src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java
./src/main/java/org/genomicsdb/importer/GenomicsDBImporterJni.java
./src/main/java/org/genomicsdb/importer/GenomicsDBImporterStreamWrapper.java
./src/main/java/org/genomicsdb/importer/MultiChromosomeIterator.java
./src/main/java/org/genomicsdb/importer/SilentByteBufferStream.java
./src/main/java/org/genomicsdb/model/CommandLineImportConfig.java
./src/main/java/org/genomicsdb/model/ImportConfig.java
./src/main/java/org/genomicsdb/model/BatchCompletionCallbackFunctionArgument.java
./src/main/java/org/genomicsdb/reader/GenomicsDBFeatureIterator.java
./src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java
./src/main/java/org/genomicsdb/reader/GenomicsDBQueryStream.java
./src/main/java/org/genomicsdb/reader/GenomicsDBTimer.java
./src/main/java/org/genomicsdb/spark/GenomicsDBConfiguration.java
./src/main/java/org/genomicsdb/spark/GenomicsDBInputFormat.java
./src/main/java/org/genomicsdb/spark/GenomicsDBInputSplit.java
./src/main/java/org/genomicsdb/spark/GenomicsDBJavaSparkFactory.java
./src/main/java/org/genomicsdb/spark/GenomicsDBPartitionInfo.java
./src/main/java/org/genomicsdb/spark/GenomicsDBQueryInfo.java
./src/main/java/org/genomicsdb/spark/GenomicsDBSchemaFactory.java
./src/main/java/org/genomicsdb/spark/GenomicsDBInput.java
./src/main/java/org/genomicsdb/Constants.java
./src/main/java/org/genomicsdb/GenomicsDBLibLoader.java
./src/main/scala/org/genomicsdb/GenomicsDBContext.scala
./src/main/scala/org/genomicsdb/GenomicsDBPartition.scala
./src/main/scala/org/genomicsdb/GenomicsDBRDD.scala
./src/main/scala/org/genomicsdb/GenomicsDBScalaSparkFactory.scala
./src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java
./src/test/java/org/genomicsdb/reader/ChrArrayFolderComparatorSpec.java
./src/test/java/org/genomicsdb/spark/GenomicsDBInputFormatTest.java
./src/test/java/org/genomicsdb/model/CommandLineImportConfigSpec.java
./src/test/java/org/genomicsdb/model/GenomicsDBCallsetsMapProtoSpec.java
./src/test/java/org/genomicsdb/model/GenomicsDBExportConfigurationSpec.java
./src/test/java/org/genomicsdb/model/GenomicsDBImportConfigurationSpec.java
./src/test/java/org/genomicsdb/model/GenomicsDBVidMappingProtoSpec.java
./src/test/java/org/genomicsdb/model/ImportConfigSpec.java
./src/test/java/org/genomicsdb/GenomicsDBTestUtils.java
)
set(JAVA_SCALA_SOURCES
${JAVA_SCALA_SOURCES}
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBRecordReader.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBSource.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBTable.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBScan.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBScanBuilder.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBBatch.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBInputPartition.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBInputPartitionReader.java
./src/main/java/org/genomicsdb/spark/sources/GenomicsDBPartitionReaderFactory.java
)
if(PROTOBUF_REGENERATE)
#Must be set here - see https://cmake.org/cmake/help/v3.3/command/set_source_files_properties.html
set_source_files_properties(${PROTOBUF_GENERATED_JAVA_SRCS} PROPERTIES GENERATED True)
#Protobuf files are generated by Maven
set(MAVEN_PROTOBUF_REGENERATE_ARGS "-Dprotoc.filepath=${PROTOBUF_PROTOC_EXECUTABLE}"
"-Dprotobuf.output.directory=${PROTOBUF_JAVA_OUTPUT_DIR}")
else()
set(JAVA_SCALA_SOURCES ${JAVA_SCALA_SOURCES} ${PROTOBUF_GENERATED_JAVA_SRCS})
set(MAVEN_PROTOBUF_REGENERATE_ARGS "")
endif()
set(MAVEN_QUIET_ARGS "")
if(MAVEN_QUIET)
set(MAVEN_QUIET_ARGS "--quiet")
endif()
set(MAVEN_ARGS
${MAVEN_QUIET_ARGS}
-Dgenomicsdb.version=${GENOMICSDB_RELEASE_VERSION}
-Dgenomicsdb_source_directory=${CMAKE_SOURCE_DIR}
-Dgenomicsdb_build_directory=${GENOMICSDB_MAVEN_BUILD_DIR}
-Dgenomicsdb_lib_directory=$
-Dprotobuf.version=${GENOMICSDB_PROTOBUF_VERSION}
${MAVEN_PROTOBUF_REGENERATE_ARGS})
if (GPG_PASSPHRASE)
set(MAVEN_ARGS
${MAVEN_ARGS}
-Dgpg.passphrase=${GPG_PASSPHRASE})
message(STATUS "Setting gpg passphrase for maven")
endif()
#Maven build - depends on dynamic library
add_custom_command(
OUTPUT ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}.jar ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-spark-${GENOMICSDB_RELEASE_VERSION}.jar ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}-allinone-spark.jar
COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/pom.xml ${CMAKE_BINARY_DIR}/pom.xml
COMMAND mvn versions:set ${MAVEN_QUIET_ARGS} -DnewVersion=${GENOMICSDB_RELEASE_VERSION}
COMMAND mvn package -DskipTests ${MAVEN_ARGS}
DEPENDS tiledbgenomicsdb ${JAVA_SCALA_SOURCES} pom.xml
WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
install(FILES
${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}.jar
${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-spark-${GENOMICSDB_RELEASE_VERSION}.jar
${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}-allinone-spark.jar
DESTINATION bin)
execute_process(
COMMAND ln -sf ${CMAKE_SOURCE_DIR}/tests ${CMAKE_BINARY_DIR})
add_test(NAME javatests
COMMAND mvn test
${MAVEN_ARGS}
WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
set(GENOMICSDB_EXAMPLE_SOURCES
${CMAKE_SOURCE_DIR}/example/java/TestGenomicsDB.java
${CMAKE_SOURCE_DIR}/example/java/TestBufferStreamGenomicsDBImporter.java
${CMAKE_SOURCE_DIR}/example/java/TestGenomicsDBSparkHDFS.java
${CMAKE_SOURCE_DIR}/example/java/TestGenomicsDBSource.java
${CMAKE_SOURCE_DIR}/example/java/TestGenomicsDBImporterWithMergedVCFHeader.java)
add_jar(genomicsdb-${GENOMICSDB_RELEASE_VERSION}-examples
SOURCES ${GENOMICSDB_EXAMPLE_SOURCES}
log4j.properties
INCLUDE_JARS ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}-allinone-spark.jar
OUTPUT_DIR ${GENOMICSDB_MAVEN_BUILD_DIR})
#Deploy to Maven central
#Cannot specify the jars in the DEPENDS clause. CMake manual specifies, quoting:
#"Do not list the output in more than one independent target that may build in parallel or
#the two instances of the rule may conflict"
#Jars are already listed as dependencies in the add_jar command (-examples)
#So, use the examples target as a dependency for this target
add_custom_target(mvn_central_deploy
COMMAND mvn ${MAVEN_ARGS} deploy
COMMENT "Deploy to Maven central"
)
add_dependencies(mvn_central_deploy genomicsdb-${GENOMICSDB_RELEASE_VERSION}-examples)
add_custom_target(mvn_local_deploy
COMMAND mvn install:install-file -Dfile=target/genomicsdb-${GENOMICSDB_RELEASE_VERSION}.jar -DpomFile=pom.xml)
add_dependencies(mvn_local_deploy genomicsdb-${GENOMICSDB_RELEASE_VERSION}-examples)
if(NOT DISABLE_MPI)
add_test(NAME CI_tests
COMMAND ${CMAKE_SOURCE_DIR}/tests/run.py
${CMAKE_BINARY_DIR}
${CMAKE_INSTALL_PREFIX}
${CMAKE_BUILD_TYPE})
endif()
endif()
GenomicsDB-1.5.3/Dockerfile 0000664 0000000 0000000 00000004310 14600153730 0015461 0 ustar 00root root 0000000 0000000 # The MIT License (MIT)
# Copyright (c) 2019-2020 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Description: Docker file for building and installing GenomicsDB
# OS currently tested are ubuntu and centos
#ARG os=ubuntu:trusty
ARG os=centos:7
FROM $os as full
ARG user=genomicsdb
ARG distributable_jar=false
# Options to enable_bindings are only java for now
# e.g. enable_bindings="java"
ARG enable_bindings=""
COPY . /build/GenomicsDB/
ENV DOCKER_BUILD=true
ENV BUILD_DISTRIBUTABLE_LIBRARY=${distributable_jar}
WORKDIR /build/GenomicsDB
RUN ./scripts/prereqs/install_prereqs.sh full &&\
useradd -r -U -m ${user} &&\
./scripts/install_genomicsdb.sh ${user} /usr/local ${distributable_jar} ${enable_bindings}
ARG os=centos:7
FROM $os as release
ARG user=genomicsdb
ARG install_dir=/usr/local
ARG distributable_jar=false
ARG enable_bindings=""
ENV BUILD_DISTRIBUTABLE_LIBRARY=${distributable_jar}
COPY ./scripts/prereqs /build
WORKDIR /build
RUN ./install_prereqs.sh release &&\
useradd -r -U -m ${user}
COPY --from=full /usr/local/bin/*genomicsdb* /usr/local/bin/gt_mpi_gather /usr/local/bin/vcf* ${install_dir}/bin/
USER ${user}
WORKDIR /home/${user}
ENTRYPOINT ["/bin/bash", "--login"]
GenomicsDB-1.5.3/Dockerfile.release 0000664 0000000 0000000 00000003214 14600153730 0017102 0 ustar 00root root 0000000 0000000 # The MIT License (MIT)
# Copyright (c) 2022 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Description: Docker file to generate GenomicsDB release jar
FROM ghcr.io/genomicsdb/genomicsdb:centos_6_prereqs_java_17
ARG GENOMICSDB_RELEASE_VERSION=""
ARG MAC_DYLIB_PATH=""
ARG USE_HDFS=""
ENV DOCKER_BUILD=true
ENV MAC_DYLIB_PATH=${MAC_DYLIB_PATH}
ENV USE_HDFS=${USE_HDFS}
ENV GENOMICSDB_RELEASE_VERSION=${GENOMICSDB_RELEASE_VERSION}
COPY . /build/GenomicsDB/
COPY libtiledbgenomicsdb.dylib ${MAC_DYLIB_PATH}
WORKDIR /build/GenomicsDB
RUN useradd -r -U -m genomicsdb &&\
./scripts/install_genomicsdb.sh genomicsdb /usr/local true java
GenomicsDB-1.5.3/Dockerfile.release_prereqs 0000664 0000000 0000000 00000002464 14600153730 0020651 0 ustar 00root root 0000000 0000000 # The MIT License (MIT)
# Copyright (c) 2022 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Description: Docker file for GenomicsDB prereqs. Base image for release
ARG os=centos:6
FROM $os
ENV BUILD_DISTRIBUTABLE_LIBRARY=true
COPY ./scripts/ /scripts
RUN /scripts/prereqs/install_prereqs.sh GenomicsDB-1.5.3/LICENSE 0000664 0000000 0000000 00000006107 14600153730 0014502 0 ustar 00root root 0000000 0000000 The MIT License (MIT)
Copyright (c) 2016-2018 Intel Corporation
Copyright (c) 2018-2020 Omics Data Automation, Inc.
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-libcsv------------------------------------------------------------------------------------------
We use libcsv (https://sourceforge.net/projects/libcsv/) to parse CSV files. libcsv
is licensed under the GNU Library or Lesser General Public License version 2.0 (LGPLv2).
So, if you are re-distributing binaries or object files, they may be subject to LGPLv2
terms. Please ensure that any binaries/object files you distribute are compliant with
LGPLv2. You can disable libcsv usage by not setting the USE_LIBCSV and LIBCSV_DIR flags
during compilation. However, your binaries/executables will not be able to import CSV
files into GenomicsDB.
-protobuf----------------------------------------------------------------------------------------
We use Google protocol buffers in GenomicsDB for representing the mapping information.
Quoting from the protobuf license
(https://github.com/google/protobuf/blob/master/LICENSE):
"Code generated by the Protocol Buffer compiler is owned by the owner of the input file
used when generating it. This code is not standalone and requires a support library to be
linked with it. This support library is itself covered by the above license."
The .proto files and the generated C++ and Java source files are covered by the license
text in lines 1-20 in this file.
If you distribute the GenomicsDB binaries with the protobuf support library linked in
statically, you must specify that the protobuf support library (in binary form) is covered
by the Protocol Buffers license (https://github.com/google/protobuf/blob/master/LICENSE).
-libuuid-----------------------------------------------------------------------------------------
We use libuuid (https://sourceforge.net/projects/libuuid/) which is licensed under the GNU Library
or Lesser General Public License version 2.0 (LGPLv2). So, if you are re-distributing binaries or
object files, they may be subject to LGPLv2 terms. Please ensure that any binaries/object files you
distribute are compliant with LGPLv2.
GenomicsDB-1.5.3/README.md 0000664 0000000 0000000 00000005545 14600153730 0014761 0 ustar 00root root 0000000 0000000 [](https://opensource.org/licenses/MIT)
[](https://genomicsdb.readthedocs.io/en/latest/)
[](https://mvnrepository.com/artifact/org.genomicsdb)
| Master | Develop |
| --- | --- |
| [](https://github.com/GenomicsDB/GenomicsDB/actions?query=branch%3Amaster) | [](https://github.com/GenomicsDB/GenomicsDB/actions?query=branch%3Adevelop) |
| [](https://codecov.io/gh/GenomicsDB/GenomicsDB) | [](https://codecov.io/gh/GenomicsDB/GenomicsDB/branch/develop) |
GenomicsDB is built on top of a fork of [htslib](https://github.com/samtools/htslib) and a tile-based array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data. GenomicsDB is a highly performant scalable data storage written in C++ for importing, querying and transforming genomic variant data. See [genomicsdb.readthedocs.io](https://genomicsdb.readthedocs.io/en/latest/) for documentation and usage.
* Supported platforms : Linux and MacOS.
* Supported filesystems : POSIX, HDFS, EMRFS(S3), GCS and Azure Blob.
Included are
* JVM/Spark wrappers that allow for streaming [VariantContext](https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/variantcontext/VariantContext.html) buffers to/from the C++ layer among other functions. GenomicsDB jars with native libraries and only zlib dependencies are regularly published on [Maven Central](https://repo1.maven.org/maven2/org/genomicsdb/genomicsdb).
* Native tools for incremental ingestion of variants in the form of VCF/BCF/CSV into GenomicsDB for performance.
* MPI and Spark support for parallel querying of GenomicsDB.
GenomicsDB is packaged into [gatk4](https://software.broadinstitute.org/gatk/documentation/article?id=11091) and benefits qualitatively from a large user base.
## External Contributions
GenomicsDB is open source and all participation is welcome.
GenomicsDB is released under the MIT License and all external
contributors are expected to grant an MIT License for their contributions.
### Checklist before creating Pull Request
Please ensure that the code is well documented in Javadoc style for Java/Scala. For Java/C/C++ code formatting, roughly adhere to the Google Style Guides. See [GenomicsDB Style Guide](Style.md)
GenomicsDB-1.5.3/Style.md 0000664 0000000 0000000 00000001167 14600153730 0015120 0 ustar 00root root 0000000 0000000 ## GenomicsDB Style Guide
For Java code, roughly adhere to [Google Java Style](https://google.github.io/styleguide/javaguide.html) and for C/C++ roughly adhere to [Google C++ Style](https://google.github.io/styleguide/cppguide.html) for consistency/readabilty
GenomicsDB Example Rules:
```
Use spaces instead of tabs.
Use 2 spaces for indenting.
Add brackets even for one line blocks e.g.
if (x>0)
do_foo();
should ideally be
if (x>0) {
do_foo();
}
Pad header e.g.
if(x>0) should be if (x>0)
while(x>0) should be while (x>0)
One half indent for class modifiers.
```
GenomicsDB-1.5.3/cmake/ 0000775 0000000 0000000 00000000000 14600153730 0014551 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/cmake/Modules/ 0000775 0000000 0000000 00000000000 14600153730 0016161 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/cmake/Modules/CheckAndSetStackProtectorStrong.cmake 0000664 0000000 0000000 00000000715 14600153730 0025367 0 ustar 00root root 0000000 0000000 include(CheckCXXCompilerFlag)
#Check -fstack-protector-strong
macro (CHECK_AND_SET_STACK_PROTECTOR_STRONG_FLAG STACK_PROTECTOR_STRONG_FOUND)
set(BACKUP_CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fstack-protector-strong")
CHECK_CXX_COMPILER_FLAG(-std=c++11 ${STACK_PROTECTOR_STRONG_FOUND})
if(NOT ${STACK_PROTECTOR_STRONG_FOUND})
set(CMAKE_CXX_FLAGS "${BACKUP_CMAKE_CXX_FLAGS}")
endif()
endmacro()
GenomicsDB-1.5.3/cmake/Modules/CheckAndSetStdCXX2011Flag.cmake 0000664 0000000 0000000 00000001527 14600153730 0023440 0 ustar 00root root 0000000 0000000 include(CheckCXXCompilerFlag)
#Check C++ 2011 support
macro (CHECK_AND_SET_STD_CXX_2011_FLAG CXX_STD_2011_FOUND)
set(BACKUP_CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
#string_view requires C++ 2017 support - most compilers that
#support string_view also support 2017 (or 201y)
set(CMAKE_CXX_FLAGS "${BACKUP_CMAKE_CXX_FLAGS} -std=c++17")
CHECK_CXX_COMPILER_FLAG(-std=c++17 ${CXX_STD_2011_FOUND})
if(NOT ${CXX_STD_2011_FOUND})
set(CMAKE_CXX_FLAGS "${BACKUP_CMAKE_CXX_FLAGS} -std=c++1y")
CHECK_CXX_COMPILER_FLAG(-std=c++1y ${CXX_STD_2011_FOUND})
if(NOT ${CXX_STD_2011_FOUND})
set(CMAKE_CXX_FLAGS "${BACKUP_CMAKE_CXX_FLAGS} -std=c++11")
CHECK_CXX_COMPILER_FLAG(-std=c++11 ${CXX_STD_2011_FOUND})
if(NOT ${CXX_STD_2011_FOUND})
set(CMAKE_CXX_FLAGS "${BACKUP_CMAKE_CXX_FLAGS}")
endif()
endif()
endif()
endmacro()
GenomicsDB-1.5.3/cmake/Modules/FindCURL.cmake 0000664 0000000 0000000 00000005315 14600153730 0020535 0 ustar 00root root 0000000 0000000 #
# cmake/Modules/FindCURL.cmake
#
# The MIT License
#
# Copyright (c) 2019 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Find the native CURL headers and libraries.
#
# CURL_INCLUDE_DIRS - where to find curl/curl.h, etc.
# CURL_LIBRARIES - List of libraries when using curl.
# CURL_FOUND - True if curl found.
# CURL_VERSION_STRING - the version of curl found (since CMake 2.8.8)
# Look for the header file.
find_path(CURL_INCLUDE_DIR NAMES curl/curl.h HINTS ${CURL_PREFIX_DIR} ${CURL_PREFIX_DIR}/include)
mark_as_advanced(CURL_INCLUDE_DIR)
if(BUILD_DISTRIBUTABLE_LIBRARY AND NOT APPLE)
find_library(CURL_LIBRARY NAMES libcurl.a
HINTS ${CURL_PREFIX_DIR} ${CURL_PREFIX_DIR}/lib64 ${CURL_PREFIX_DIR}/lib)
else()
find_library(CURL_LIBRARY NAMES curl libcurl
HINTS ${CURL_PREFIX_DIR} ${CURL_PREFIX_DIR}/lib64 ${CURL_PREFIX_DIR}/lib
)
endif()
mark_as_advanced(CURL_LIBRARY)
if(CURL_INCLUDE_DIR)
foreach(_curl_version_header curlver.h curl.h)
if(EXISTS "${CURL_INCLUDE_DIR}/curl/${_curl_version_header}")
file(STRINGS "${CURL_INCLUDE_DIR}/curl/${_curl_version_header}" curl_version_str REGEX "^#define[\t ]+LIBCURL_VERSION[\t ]+\".*\"")
string(REGEX REPLACE "^#define[\t ]+LIBCURL_VERSION[\t ]+\"([^\"]*)\".*" "\\1" CURL_VERSION_STRING "${curl_version_str}")
unset(curl_version_str)
break()
endif()
endforeach()
endif()
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(CURL
REQUIRED_VARS CURL_LIBRARY CURL_INCLUDE_DIR
VERSION_VAR CURL_VERSION_STRING)
if(CURL_FOUND)
set(CURL_LIBRARIES ${CURL_LIBRARY})
set(CURL_INCLUDE_DIRS ${CURL_INCLUDE_DIR})
endif()
GenomicsDB-1.5.3/cmake/Modules/FindGPerftools.cmake 0000664 0000000 0000000 00000004332 14600153730 0022052 0 ustar 00root root 0000000 0000000 #
# FindGPerftools.cmake
#
# The MIT License
#
# Copyright (c) 2022 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Determine compiler flags for gperftools
# Once done this will define
# GPERFTOOLS_FOUND - gperftools found
#
if (USE_GPERFTOOLS)
find_path(GPERFTOOLS_INCLUDE_DIR NAMES gperftools/profiler.h HINTS "${GPERFTOOLS_DIR}" "${GPERFTOOLS_DIR}/include")
find_library(GPERFTOOLS_PROFILER_LIBRARY NAMES profiler HINTS "${GPERFTOOLS_DIR}" "${GPERFTOOLS_DIR}/lib64" "${GPERFTOOLS_DIR}/lib")
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(GPerftools "Could not find gperftools headers and/or libraries ${DEFAULT_MSG}" GPERFTOOLS_PROFILER_LIBRARY GPERFTOOLS_INCLUDE_DIR)
endif()
if (USE_GPERFTOOLS_HEAP)
find_path(GPERFTOOLS_INCLUDE_DIR NAMES gperftools/tcmalloc.h HINTS "${GPERFTOOLS_DIR}" "${GPERFTOOLS_DIR}/include")
find_library(GPERFTOOLS_HEAP_PROFILER_LIBRARY NAMES tcmalloc HINTS "${GPERFTOOLS_DIR}" "${GPERFTOOLS_DIR}/lib64" "${GPERFTOOLS_DIR}/lib")
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(GPerftools "Could not find gperftools heap headers and/or libraries ${DEFAULT_MSG}" GPERFTOOLS_HEAP_PROFILER_LIBRARY GPERFTOOLS_INCLUDE_DIR)
endif()
GenomicsDB-1.5.3/cmake/Modules/FindIPP.cmake 0000664 0000000 0000000 00000001031 14600153730 0020407 0 ustar 00root root 0000000 0000000 # Determine path to IPP libraries for Zlib
# Once done this will define
# LIBIPP_FOUND - IPP found
find_library(LIBIPPDC_LIBRARY NAMES libippdc.a ippdc HINTS "${IPPROOT}/lib/intel64/")
find_library(LIBIPPS_LIBRARY NAMES libipps.a ipps HINTS "${IPPROOT}/lib/intel64/")
find_library(LIBIPPCORE_LIBRARY NAMES libippcore.a ippcore HINTS "${IPPROOT}/lib/intel64/")
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(IPP "Could not find IPP libraries ${DEFAULT_MSG}" LIBIPPDC_LIBRARY LIBIPPS_LIBRARY LIBIPPCORE_LIBRARY)
GenomicsDB-1.5.3/cmake/Modules/FindOpenMPv4.cmake 0000664 0000000 0000000 00000001642 14600153730 0021377 0 ustar 00root root 0000000 0000000 # Determine if OpenMP specification v4 is supported by the C/C++ compiler
# Once done this will define
# OPENMPV4_FOUND - OpenMP v4 found
# OpenMP_C_FLAGS
# OpenMP_CXX_FLAGS
include(CheckCSourceCompiles)
find_package(OpenMP QUIET)
set(OpenMPv4_C_TEST_SOURCE
"
#include
#include
/*Define custom reduction operation*/
int main()
{
int i = 0;
int A[10];
int sum = 0;
#pragma omp declare reduction ( sum_up : int : omp_out += omp_in ) initializer(omp_priv = 0)
#pragma omp parallel for default(shared) reduction(sum_up : sum)
for(i=0;i<10;++i)
sum += A[i];
return 0;
}
")
if(NOT OPENMP_FOUND)
set(OPENMPV4_FOUND False)
else()
set(SAFE_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
set(CMAKE_REQUIRED_FLAGS "${OpenMP_C_FLAGS}")
check_c_source_compiles("${OpenMPv4_C_TEST_SOURCE}" OPENMPV4_FOUND)
set(CMAKE_REQUIRED_FLAGS "${SAFE_CMAKE_REQUIRED_FLAGS}")
endif()
GenomicsDB-1.5.3/cmake/Modules/FindProtobufWrapper.cmake 0000664 0000000 0000000 00000007411 14600153730 0023130 0 ustar 00root root 0000000 0000000 #
# CMakeLists.txt
#
# The MIT License
#
# Copyright (c) 2019-2021 Omics Data Automation, Inc.
# Copyright (c) 2023 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
add_custom_target(protobuf_ep)
message(CHECK_START "Try finding Protobuf Library")
if(PROTOBUF_ROOT_DIR)
set(PROTOBUF_PREFIX ${PROTOBUF_ROOT_DIR})
elseif(DEFINED ENV{PROTOBUF_ROOT_DIR})
set(PROTOBUF_PREFIX $ENV{PROTOBUF_ROOT_DIR})
endif()
set(PROTOBUF_BIN_DIR ${PROTOBUF_PREFIX}/bin)
set(PROTOBUF_LIB_DIR ${PROTOBUF_PREFIX}/${CMAKE_INSTALL_LIBDIR})
set(PROTOBUF_INCLUDE_DIR ${PROTOBUF_PREFIX}/include)
if(EXISTS ${PROTOBUF_BIN_DIR}/protoc AND EXISTS ${PROTOBUF_LIB_DIR} AND EXISTS ${PROTOBUF_LIB_DIR} AND EXISTS ${PROTOBUF_INCLUDE_DIR})
find_package(Protobuf PATHS ${PROTOBUF_PREFIX})
endif()
if(NOT Protobuf_FOUND AND NOT PROTOBUF_PREFIX)
message(CHECK_FAIL "not found")
message(FATAL_ERROR "Try invoking cmake with -DPROTOBUF_ROOT_DIR=/path/to/protobuf or -DCMAKE_INSTALL_PREFIX=/path/to/protobuf or set environment variable PROTOBUF_ROOT_DIR before invoking cmake")
elseif(Protobuf_FOUND)
message(CHECK_PASS "found ${Protobuf_VERSION}")
else()
# Try building from source
# Workaround for issues with semicolon separated substrings to ExternalProject_Add
# https://discourse.cmake.org/t/how-to-pass-cmake-osx-architectures-to-externalproject-add/2262
if(CMAKE_OSX_ARCHITECTURES)
if(CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" AND CMAKE_OSX_ARCHITECTURES MATCHES "arm64")
set(CMAKE_OSX_ARGS -DCMAKE_OSX_ARCHITECTURES=arm64$x86_64)
elseif(NOT CMAKE_OSX_ARCHITECTURES STREQUAL CMAKE_SYSTEM_PROCESSOR)
# Compile for both architectures as protoc is a binary and needs to run on the host for source code generation
set(CMAKE_OSX_ARGS -DCMAKE_OSX_ARCHITECTURES=arm64$x86_64)
else()
set(CMAKE_OSX_ARGS -DCMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES})
endif()
endif()
message(CHECK_PASS "not found, building Protobuf ${GENOMICSDB_PROTOBUF_VERSION} as an external project")
include(ExternalProject)
ExternalProject_Add(protobuf_build
PREFIX ${PROTOBUF_PREFIX}
URL ${PROTOBUF_URL}
SOURCE_SUBDIR cmake
CMAKE_ARGS ${CMAKE_OSX_ARGS}
-Dprotobuf_BUILD_TESTS=OFF
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_PREFIX=${PROTOBUF_PREFIX}
-DCMAKE_POSITION_INDEPENDENT_CODE=ON
-DCMAKE_C_VISIBILITY_PRESET=hidden
-DCMAKE_CXX_VISIBILITY_PRESET=hidden
-DCMAKE_VISIBILITY_INLINES_HIDDEN=TRUE
-DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}
)
add_dependencies(protobuf_ep protobuf_build)
endif()
set(PROTOBUF_PROTOC_EXECUTABLE ${PROTOBUF_BIN_DIR}/protoc)
set(PROTOBUF_INCLUDE_DIRS ${PROTOBUF_INCLUDE_DIR})
set(PROTOBUF_LIBRARIES ${PROTOBUF_LIB_DIR}/${CMAKE_STATIC_LIBRARY_PREFIX}protobuf${CMAKE_STATIC_LIBRARY_SUFFIX})
GenomicsDB-1.5.3/cmake/Modules/FindRapidJSON.cmake 0000664 0000000 0000000 00000004412 14600153730 0021516 0 ustar 00root root 0000000 0000000 #
# FindRapidJSON.cmake
#
# The MIT License
#
# Copyright (c) 2020 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Determine compiler flags for RapidJSON
# Once done this will define
# RAPIDJSON_FOUND - RapidJSON found
# RapidJSON_C_FLAGS
# RapidJSON_CXX_FLAGS
# Update git submodule if necessary
if(NOT EXISTS "${RAPIDJSON_INCLUDE_DIR}")
MESSAGE(STATUS "Installing submodule RapidJSON at ${CMAKE_SOURCE_DIR}/dependencies")
execute_process(
COMMAND git submodule update --init ${CMAKE_SOURCE_DIR}/dependencies/RapidJSON
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
RESULT_VARIABLE submodule_update_exit_code)
if(NOT(submodule_update_exit_code EQUAL 0))
message(FATAL_ERROR "Failure to update git submodule RapidJSON")
endif()
set(RAPIDJSON_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/dependencies/RapidJSON/include" CACHE PATH "Path to RapidJSON include directory" FORCE)
endif()
find_path(RAPIDJSON_INCLUDE_DIR
NAMES rapidjson/rapidjson.h
PATHS "${RAPIDJSON_INCLUDE_DIR}"
CMAKE_FIND_ROOT_PATH_BOTH)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(RapidJSON "Could not find RapidJSON header: rapidjson/rapidjson.h - specify the variable RAPIDJSON_INCLUDE_DIR to point to the directory /include"
RAPIDJSON_INCLUDE_DIR)
GenomicsDB-1.5.3/cmake/Modules/FindSpdlog.cmake 0000664 0000000 0000000 00000004366 14600153730 0021225 0 ustar 00root root 0000000 0000000 #
# FindSpdlog.cmake
#
# The MIT License
#
# Copyright (c) 2020 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Find SpdLog include files to include with GenomicsDB
# Once done, this will define
# SPDLOG_FOUND
# SPDLOG_INCLUDE_DIR
# Update git submodule if necessary
if(NOT EXISTS "${SPDLOG_INCLUDE_DIR}")
MESSAGE(STATUS "Installing submodule SpdLog at ${CMAKE_SOURCE_DIR}/dependencies")
execute_process(
COMMAND git submodule update --init ${CMAKE_SOURCE_DIR}/dependencies/spdlog
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
RESULT_VARIABLE submodule_update_exit_code)
if(NOT(submodule_update_exit_code EQUAL 0))
message(FATAL_ERROR "Failure to update git submodule spdlog")
endif()
set(SPDLOG_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/dependencies/spdlog/include" CACHE PATH "Path to SpdLog include directory" FORCE)
endif()
find_path(
SPDLOG_INCLUDE_DIR NAMES spdlog/spdlog.h
HINTS "${SPDLOG_INCLUDE_DIR}"
PATHS "${CMAKE_SOURCE_DIR}/dependencies/spdlog/include"
CMAKE_FIND_ROOT_PATH_BOTH)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(Spdlog "Could not find SpdLog header: spdlog/spdlog.h - specify the variable SPDLOG_INCLUDE_DIR to point to the directory /include" SPDLOG_INCLUDE_DIR)
GenomicsDB-1.5.3/cmake/Modules/FindStringView.cmake 0000664 0000000 0000000 00000001473 14600153730 0022072 0 ustar 00root root 0000000 0000000 # Once done this will define
# STRING_VIEW_FOUND if string_view found
include(CheckCXXSourceCompiles)
set(STRING_VIEW_SRC
"
#include
int main() {
std::string_view(\"qwerty\");
return 0;
}
"
)
set(STRING_VIEW_EXPERIMENTAL_SRC
"
#include
int main() {
std::experimental::string_view(\"qwerty\");
return 0;
}
"
)
check_cxx_source_compiles("${STRING_VIEW_SRC}" STRING_VIEW_FOUND)
if(NOT STRING_VIEW_FOUND)
check_cxx_source_compiles("${STRING_VIEW_EXPERIMENTAL_SRC}" STRING_VIEW_EXPERIMENTAL_FOUND)
if(STRING_VIEW_EXPERIMENTAL_FOUND)
message(STATUS "experimental/string_view found")
add_definitions(-DSTRING_VIEW_EXPERIMENTAL_FOUND=1)
endif()
else()
message(STATUS "string_view found")
add_definitions(-DSTRING_VIEW_FOUND=1)
endif()
GenomicsDB-1.5.3/cmake/Modules/FindTileDB.cmake 0000664 0000000 0000000 00000006762 14600153730 0021102 0 ustar 00root root 0000000 0000000 #
# FindTileDB.cmake
#
# The MIT License
#
# Copyright (c) 2016 MIT and Intel Corporation
# Copyright (c) 2019-2020 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Determine compiler flags for TileDB
# Once done this will define
# TILEDB_FOUND - TileDB found
# Update git submodule if necessary
if((DEFINED TILEDB_SOURCE_DIR) AND (NOT "${TILEDB_SOURCE_DIR}" STREQUAL "") AND (NOT EXISTS "${TILEDB_SOURCE_DIR}/CMakeLists.txt"))
MESSAGE(STATUS "Installing submodule TileDB at ${CMAKE_SOURCE_DIR}/dependencies")
execute_process(
COMMAND git submodule update --recursive --init ${CMAKE_SOURCE_DIR}/dependencies/TileDB
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
RESULT_VARIABLE submodule_update_exit_code)
if(NOT(submodule_update_exit_code EQUAL 0))
message(FATAL_ERROR "Failure to update git submodule TileDB")
endif()
set(TILEDB_SOURCE_DIR "${CMAKE_SOURCE_DIR}/dependencies/TileDB" CACHE PATH "Path to TileDB source directory" FORCE)
endif()
if(CMAKE_BUILD_TYPE STREQUAL "Release")
#TileDB c-api returns a tiledb_errmsg which is what GenomicsDB should rely on
set(TILEDB_VERBOSE FALSE CACHE BOOL "Suppress TileDB Verbosity for GenomicsDB" FORCE)
endif()
set(TILEDB_DISABLE_TESTING True)
#Zlib
find_package(ZLIB REQUIRED)
#ZStd
set(ENABLE_ZSTD TRUE CACHE BOOL "Enable ZStd" FORCE)
if(BUILD_DISTRIBUTABLE_LIBRARY)
set(OPENSSL_USE_STATIC_LIBS True)
endif()
find_package(OpenSSL REQUIRED) #now performed inside TileDB
#libuuid
find_package(libuuid REQUIRED)
include(FindPackageHandleStandardArgs)
set(TILEDB_DISABLE_TESTS True CACHE BOOL "Disable TileDB Testing")
#Build if TileDB source directory specified
if(TILEDB_SOURCE_DIR)
#OpenMP
if(DISABLE_OPENMP)
set(USE_OPENMP False CACHE BOOL "Disable OpenMP" FORCE)
else()
set(USE_OPENMP True CACHE BOOL "Enable OpenMP" FORCE)
endif()
find_path(TILEDB_INCLUDE_DIR NAMES tiledb.h HINTS "${TILEDB_SOURCE_DIR}/core/include/c_api")
find_package_handle_standard_args(TileDB "Could not find TileDB headers ${DEFAULT_MSG}" TILEDB_INCLUDE_DIR)
add_subdirectory(${TILEDB_SOURCE_DIR} dependencies/TileDB EXCLUDE_FROM_ALL)
else()
find_path(TILEDB_INCLUDE_DIR NAMES "tiledb.h" HINTS "${TILEDB_INSTALL_DIR}/include")
find_library(TILEDB_LIBRARY NAMES libtiledb.a tiledb HINTS "${TILEDB_INSTALL_DIR}" "${TILEDB_INSTALL_DIR}/lib64" "${TILEDB_INSTALL_DIR}/lib")
find_package_handle_standard_args(TileDB "Could not find TileDB headers and/or libraries ${DEFAULT_MSG}" TILEDB_INCLUDE_DIR TILEDB_LIBRARY)
endif()
GenomicsDB-1.5.3/cmake/Modules/Findfmt.cmake 0000664 0000000 0000000 00000001575 14600153730 0020562 0 ustar 00root root 0000000 0000000 # Determine compiler flags for fmt library
# Once done this will define
# FMT_FOUND - fmt found
if(USING_FMT_BUNDLED_WITH_SPDLOG)
#fmt headers are in dependencies/spdlog/include/spdlog/fmt/bundled - source files will include "fmt/bundled/format.h"
find_path(FMT_INCLUDE_DIR NAMES spdlog/fmt/bundled/core.h HINTS "${FMT_ROOT_DIR}/include" "${FMT_ROOT_DIR}")
else()
find_path(FMT_INCLUDE_DIR NAMES fmt/core.h HINTS "${FMT_ROOT_DIR}/include" "${FMT_ROOT_DIR}")
endif()
if(BUILD_DISTRIBUTABLE_LIBRARY)
find_library(FMT_LIBRARY NAMES libfmt.a fmt HINTS "${FMT_ROOT_DIR}/lib64" "${FMT_ROOT_DIR}/lib" "${FMT_ROOT_DIR}")
else()
find_library(FMT_LIBRARY NAMES fmt HINTS "${FMT_ROOT_DIR}/lib64" "${FMT_ROOT_DIR}/lib" "${FMT_ROOT_DIR}")
endif()
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(fmt "Could not find fmt library headers ${DEFAULT_MSG}" FMT_INCLUDE_DIR)
GenomicsDB-1.5.3/cmake/Modules/Findhtslib.cmake 0000664 0000000 0000000 00000014320 14600153730 0021251 0 ustar 00root root 0000000 0000000 #
# FindTileDB.cmake
#
# The MIT License
#
# Copyright (c) 2020-2021 Omics Data Automation, Inc.
# Copyright (c) 2023 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Determine compiler flags for htslib
# Once done this will define
# HTSLIB_FOUND - htslib found
include(FindPackageHandleStandardArgs)
# Update git submodule if necessary
if((DEFINED HTSLIB_SOURCE_DIR) AND (NOT "${HTSLIB_SOURCE_DIR}" STREQUAL "") AND (NOT EXISTS "${HTSLIB_SOURCE_DIR}/htslib/vcf.h"))
MESSAGE(STATUS "Installing submodule htslib at ${CMAKE_SOURCE_DIR}/dependencies")
execute_process(
COMMAND git submodule update --init ${CMAKE_SOURCE_DIR}/dependencies/htslib
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
RESULT_VARIABLE submodule_update_exit_code)
if(NOT(submodule_update_exit_code EQUAL 0))
message(FATAL_ERROR "Failure to update git submodule htslib")
endif()
set(HTSLIB_SOURCE_DIR "${CMAKE_SOURCE_DIR}/dependencies/htslib" CACHE PATH "Path to htslib source directory" FORCE)
endif()
function(build_universal_htslib arch1 arch2)
add_custom_target(htslib COMMAND
echo "Building universal library in HTSLIB_INSTALL_DIR=${HTSLIB_INSTALL_DIR} for ${arch1} ${arch2}" &&
lipo -create ${HTSLIB_BUILD_PREFIX}_${arch1}/libhts.a ${HTSLIB_BUILD_PREFIX}_${arch2}/libhts.a -output ${HTSLIB_LIBRARY})
add_dependencies(htslib htslib_${arch1} htslib_${arch2})
endfunction()
function(build_htslib arch)
if (NOT ${arch} STREQUAL "")
set(SUFFIX _${arch})
set(ARCH_C_FLAGS "-arch ${arch} ${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS}")
if (NOT arch STREQUAL CMAKE_SYSTEM_PROCESSOR)
set(ARCH_HOST_FLAGS "--host=${CMAKE_SYSTEM_PROCESSOR}")
endif()
else()
set(ARCH_C_FLAGS ${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS})
endif()
ExternalProject_Add(htslib${SUFFIX}
PREFIX ${HTSLIB_BUILD_PREFIX}${SUFFIX}
DOWNLOAD_COMMAND ""
SOURCE_DIR ${HTSLIB_SOURCE_DIR}
BINARY_DIR ${HTSLIB_BUILD_PREFIX}${SUFFIX}
UPDATE_COMMAND autoreconf -i ${HTSLIB_SOURCE_DIR}
PATCH_COMMAND ""
CONFIGURE_COMMAND ${HTSLIB_ENV} ${HTSLIB_SOURCE_DIR}/configure ${ARCH_HOST_FLAGS}
CFLAGS=${ARCH_C_FLAGS}
LDFLAGS=${HTSLIB_${CMAKE_BUILD_TYPE}_LDFLAGS}
CC=${CMAKE_C_COMPILER} AR=${CMAKE_AR} RANLIB=${CMAKE_RANLIB}
--disable-lzma --disable-bz2 --disable-s3 --disable-gcs --without-libdeflate
BUILD_COMMAND
COMMAND ${CMAKE_COMMAND} -E make_directory cram
COMMAND ${CMAKE_COMMAND} -E copy ${HTSLIB_SOURCE_DIR}/version.sh .
COMMAND ${HTSLIB_ENV} $(MAKE) -f ${HTSLIB_SOURCE_DIR}/Makefile VPATH=${HTSLIB_SOURCE_DIR} SOURCE_DIR=${HTSLIB_SOURCE_DIR} AR=${CMAKE_AR} libhts.a
INSTALL_COMMAND ""
)
endfunction()
#Build if htslib source directory specified
if(HTSLIB_SOURCE_DIR)
set(HTSLIB_Debug_CFLAGS " -Wall -fPIC -DDEBUG -g3 -gdwarf-3 -DVCF_ALLOW_INT64=1") #will be picked if compiling in debug mode
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(HTSLIB_Debug_CFLAGS "${HTSLIB_Debug_CFLAGS} -Wno-expansion-to-defined -Wno-nullability-completeness")
endif()
set(HTSLIB_Coverage_CFLAGS "${HTSLIB_Debug_CFLAGS}")
set(HTSLIB_Release_CFLAGS " -Wall -fPIC -O3 -DVCF_ALLOW_INT64=1")
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(HTSLIB_Release_CFLAGS "${HTSLIB_Release_CFLAGS} -Wno-expansion-to-defined -Wno-nullability-completeness")
endif()
if(APPLE)
set(HTSLIB_LDFLAGS " -L /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib")
endif()
set(HTSLIB_Debug_LDFLAGS "-g3 -gdwarf-3 ${HTSLIB_LDFLAGS}")
set(HTSLIB_Coverage_LDFLAGS "${HTSLIB_Debug_LDFLAGS}")
set(HTSLIB_Release_LDFLAGS "${HTSLIB_LDFLAGS}")
include(ExternalProject)
set(HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS "${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS} -I${OPENSSL_INCLUDE_DIR} -I${CURL_INCLUDE_DIRS}")
set(HTSLIB_LIBRARY ${CMAKE_BINARY_DIR}/libhts.a)
if(APPLE)
if(BUILD_DISTRIBUTABLE_LIBRARY)
set(HTSLIB_ENV "MACOSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}")
endif()
endif()
set(HTSLIB_BUILD_PREFIX ${CMAKE_BINARY_DIR}/dependencies/htslib)
set(HTSLIB_LIBRARY ${CMAKE_BINARY_DIR}/libhts.a)
if(APPLE AND CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" AND CMAKE_OSX_ARCHITECTURES MATCHES "arm64")
build_htslib("x86_64")
build_htslib("arm64")
build_universal_htslib("x86_64" "arm64")
elseif(APPLE AND CMAKE_OSX_ARCHITECTURES)
build_htslib(${CMAKE_OSX_ARCHITECTURES})
add_custom_target(htslib COMMAND cp ${HTSLIB_BUILD_PREFIX}_${CMAKE_OSX_ARCHITECTURES}/libhts.a ${HTSLIB_LIBRARY})
add_dependencies(htslib htslib_${CMAKE_OSX_ARCHITECTURES})
else()
build_htslib("")
add_custom_command(TARGET htslib POST_BUILD COMMAND cp ${HTSLIB_BUILD_PREFIX}/libhts.a ${HTSLIB_LIBRARY} VERBATIM)
endif()
find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_SOURCE_DIR}" CMAKE_FIND_ROOT_PATH_BOTH NO_DEFAULT_PATH)
find_package_handle_standard_args(htslib "Could not find htslib headers ${DEFAULT_MSG}" HTSLIB_INCLUDE_DIR)
else()
find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_INSTALL_DIR}")
find_library(HTSLIB_LIBRARY NAMES libhts.a hts HINTS "${HTSLIB_INSTALL_DIR}")
find_package_handle_standard_args(htslib "Could not find htslib headers and/or libraries ${DEFAULT_MSG}" HTSLIB_INCLUDE_DIR HTSLIB_LIBRARY)
endif()
GenomicsDB-1.5.3/cmake/Modules/Findlibcsv.cmake 0000664 0000000 0000000 00000003123 14600153730 0021245 0 ustar 00root root 0000000 0000000 #
# Findlibcsv.cmake
#
# The MIT License
#
# Copyright (c) 2022 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Determine compiler flags for libcsv
# Once done this will define
# LIBCSV_FOUND - libcsv found
find_path(LIBCSV_INCLUDE_DIR NAMES csv.h HINTS "${LIBCSV_DIR}/include" "${LIBCSV_DIR}")
find_library(LIBCSV_LIBRARY NAMES csv HINTS "${LIBCSV_DIR}/lib" "${LIBCSV_DIR}/.libs" "${LIBCSV_DIR}")
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(libcsv "Could not find libcsv headers and/or libraries ${DEFAULT_MSG}" LIBCSV_LIBRARY LIBCSV_INCLUDE_DIR)
GenomicsDB-1.5.3/cmake/Modules/Findlibdbi.cmake 0000664 0000000 0000000 00000002646 14600153730 0021221 0 ustar 00root root 0000000 0000000 # Determine compiler flags for libdbi
# Once done this will define
# LIBDBI_FOUND - libdbi found
find_path(LIBDBI_INCLUDE_DIR NAMES dbi/dbi.h HINTS "${LIBDBI_DIR}/include")
find_library(LIBPGSQL_DRIVER_LIBRARY NAMES dbdpgsql HINTS "${LIBDBI_DIR}/lib/dbd")
find_library(LIBDBI_DEV_LIBRARY NAMES dbi HINTS "${LIBDBI_DIR}/lib")
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(libdbi "Could not find libdbi headers and/or libraries ${DEFAULT_MSG}" LIBDBI_INCLUDE_DIR LIBDBI_DEV_LIBRARY LIBPGSQL_DRIVER_LIBRARY)
if(LIBDBI_FOUND)
include(CheckCSourceCompiles)
file(READ ${CMAKE_SOURCE_DIR}/cmake/Modules/libdbi_test_program.c LIBDBI_C_TEST_SOURCE)
set(SAFE_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
set(CMAKE_REQUIRED_FLAGS "-I${LIBDBI_INCLUDE_DIR}")
set(SAFE_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
set(CMAKE_REQUIRED_LIBRARIES ${LIBPGSQL_DRIVER_LIBRARY} ${LIBDBI_DEV_LIBRARY})
check_c_source_compiles("${LIBDBI_C_TEST_SOURCE}" LIBDBI_TEST_PROGRAM_COMPILES)
if(NOT LIBDBI_TEST_PROGRAM_COMPILES)
message(STATUS "libdbi headers and libraries found; however, test program fails to compile. GenomicsDB requires libdbi >= 0.9.0.")
message(STATUS "Mapping DB support disabled")
unset(LIBDBI_FOUND)
endif()
set(CMAKE_REQUIRED_FLAGS "${SAFE_CMAKE_REQUIRED_FLAGS}")
set(CMAKE_REQUIRED_LIBRARIES "${SAFE_CMAKE_REQUIRED_LIBRARIES}")
endif()
GenomicsDB-1.5.3/cmake/Modules/Findlibuuid.cmake 0000664 0000000 0000000 00000003717 14600153730 0021431 0 ustar 00root root 0000000 0000000 #
# cmake Module for libuuid
#
# The MIT License
#
# Copyright (c) 2023 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Determine compiler flags for libuuid
# Once done this will define
# LIBUUID_FOUND - libuuid found
find_path(LIBUUID_INCLUDE_DIR NAMES uuid/uuid.h HINTS "${LIBUUID_DIR}/include" "${LIBUUID_DIR}")
if(APPLE)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(libuuid "Could not find libuuid headers ${DEFAULT_MSG}" LIBUUID_INCLUDE_DIR)
else()
if(BUILD_DISTRIBUTABLE_LIBRARY)
find_library(LIBUUID_LIBRARY NAMES libuuid.a uuid HINTS "${LIBUUID_DIR}/lib64" "${LIBUUID_DIR}/lib" "${LIBUUID_DIR}")
else()
find_library(LIBUUID_LIBRARY NAMES uuid HINTS "${LIBUUID_DIR}/lib64" "${LIBUUID_DIR}/lib" "${LIBUUID_DIR}")
endif()
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(libuuid "Could not find libuuid headers and/or libraries ${DEFAULT_MSG}" LIBUUID_INCLUDE_DIR LIBUUID_LIBRARY)
endif()
GenomicsDB-1.5.3/cmake/Modules/Findsafestringlib.cmake 0000664 0000000 0000000 00000001065 14600153730 0022622 0 ustar 00root root 0000000 0000000 # Determine compiler flags for libuuid
# Once done this will define
# SAFESTRINGLIB_FOUND - libuuid found
find_path(SAFESTRINGLIB_INCLUDE_DIR NAMES safe_mem_lib.h HINTS "${SAFESTRINGLIB_DIR}/include")
find_library(SAFESTRINGLIB_LIBRARY NAMES libsafestring.a safestring HINTS "${SAFESTRINGLIB_DIR}/lib64"
"${SAFESTRINGLIB_DIR}/lib" "${SAFESTRINGLIB_DIR}")
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(safestringlib "Could not find safestring headers and/or libraries ${DEFAULT_MSG}" SAFESTRINGLIB_INCLUDE_DIR
SAFESTRINGLIB_LIBRARY)
GenomicsDB-1.5.3/cmake/Modules/libdbi_test_program.c 0000664 0000000 0000000 00000001135 14600153730 0022340 0 ustar 00root root 0000000 0000000 #include
#include
int main() {
dbi_conn conn;
dbi_result result;
dbi_inst instance;
dbi_initialize_r(NULL, &instance);
conn = dbi_conn_new_r("pgsql", instance);
dbi_conn_set_option(conn, "host", "localhost");
if (dbi_conn_connect(conn) < 0)
exit(0);
else
{
result = dbi_conn_query(conn, "SELECT * from table");
if (result) {
while (dbi_result_next_row(result)) {
unsigned idnumber = dbi_result_get_uint(result, "id");
}
dbi_result_free(result);
}
dbi_conn_close(conn);
}
dbi_shutdown_r(instance);
return 0;
}
GenomicsDB-1.5.3/dependencies/ 0000775 0000000 0000000 00000000000 14600153730 0016117 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/dependencies/RapidJSON/ 0000775 0000000 0000000 00000000000 14600153730 0017650 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/dependencies/TileDB/ 0000775 0000000 0000000 00000000000 14600153730 0017222 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/dependencies/htslib/ 0000775 0000000 0000000 00000000000 14600153730 0017404 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/dependencies/spdlog/ 0000775 0000000 0000000 00000000000 14600153730 0017407 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/docs/ 0000775 0000000 0000000 00000000000 14600153730 0014421 5 ustar 00root root 0000000 0000000 GenomicsDB-1.5.3/docs/Doxyfile 0000664 0000000 0000000 00000324054 14600153730 0016137 0 ustar 00root root 0000000 0000000 # Doxyfile 1.8.13
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
# that follow. The default is UTF-8 which is also the encoding used for all text
# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
# for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = "GenomicsDB"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER =
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF =
# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
# in the documentation. The maximum height of the logo should not exceed 55
# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
# the logo to the output directory.
PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = doxydocs
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
CREATE_SUBDIRS = NO
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF = "The $name class" \
"The $name widget" \
"The $name file" \
is \
provides \
specifies \
contains \
represents \
a \
an \
the
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = YES
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
# page for each member. If set to NO, the documentation of a member will be part
# of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 4
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
ALIASES =
# This tag can be used to specify a number of word-keyword mappings (TCL only).
# A mapping has the form "name=value". For example adding "class=itcl::class"
# will allow you to use the command class in the itcl::class meaning.
TCL_SUBST =
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
# Fortran. In the later case the parser tries to guess whether the code is fixed
# or free formatted code, this is the default for Fortran type files), VHDL. For
# instance to make doxygen treat .inc files as Fortran files (default is PHP),
# and .f files as C (default is Fortran), use: inc=Fortran f=C.
#
# Note: For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen.
EXTENSION_MAPPING =
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See http://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
# to that level are automatically included in the table of contents, even if
# they do not have an id attribute.
# Note: This feature currently applies only to Markdown headings.
# Minimum value: 0, maximum value: 99, default value: 0.
# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
TOC_INCLUDE_HEADINGS = 0
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by putting a % sign in front of the word or
# globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = NO
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = NO
# If one adds a struct or class to a group and this option is enabled, then also
# any nested class or struct is added to the same group. By default this option
# is disabled and one has to add nested compounds explicitly via \ingroup.
# The default value is: NO.
GROUP_NESTED_COMPOUNDS = NO
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = NO
# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO,
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = YES
# This flag is only useful for Objective-C code. If set to YES, local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO, only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO, these classes will be included in the various overviews. This option
# has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# (class|struct|union) declarations. If set to NO, these declarations will be
# included in the documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = NO
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO, these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = NO
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
# names in lower-case letters. If set to YES, upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
# The default value is: system dependent.
CASE_SENSE_NAMES = YES
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES, the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
# append additional text to a page's title, such as Class Reference. If set to
# YES the compound reference will be hidden.
# The default value is: NO.
HIDE_COMPOUND_REFERENCE= NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = NO
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
# list. This list is created by putting \todo commands in the documentation.
# The default value is: YES.
GENERATE_TODOLIST = YES
# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
# list. This list is created by putting \test commands in the documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = YES
# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= YES
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if ... \endif and \cond
# ... \endcond blocks.
ENABLED_SECTIONS =
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 30
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES, the
# list will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE =
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
QUIET = NO
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO, doxygen will only warn about wrong or incomplete
# parameter documentation, but not about the absence of documentation.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
# a warning is encountered.
# The default value is: NO.
WARN_AS_ERROR = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = ../src/main/cpp \
../src/main/java
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see: http://www.gnu.org/software/libiconv) for the list of
# possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# read by doxygen.
#
# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
FILE_PATTERNS = *.c \
*.cc \
*.cxx \
*.cpp \
*.c++ \
*.java \
*.ii \
*.ixx \
*.ipp \
*.i++ \
*.inl \
*.idl \
*.ddl \
*.odl \
*.h \
*.hh \
*.hxx \
*.hpp \
*.h++ \
*.cs \
*.d \
*.php \
*.php4 \
*.php5 \
*.phtml \
*.inc \
*.m \
*.markdown \
*.md \
*.mm \
*.dox \
*.py \
*.pyw \
*.f90 \
*.f95 \
*.f03 \
*.f08 \
*.f \
*.for \
*.tcl \
*.vhd \
*.vhdl \
*.ucf \
*.qsf
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS =
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS = *
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = NO
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH =
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
#
#
# where is the value of the INPUT_FILTER tag, and is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
FILTER_PATTERNS =
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = NO
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# function all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = NO
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = NO
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see http://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
# cost of reduced performance. This can be particularly helpful with template
# rich C++ code for which doxygen's built-in parser lacks the necessary type
# information.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse-libclang=ON option for CMake.
# The default value is: NO.
CLANG_ASSISTED_PARSING = NO
# If clang assisted parsing is enabled you can provide the compiler with command
# line options that you would normally use when invoking the compiler. Note that
# the include paths will already be set by doxygen for the files and directories
# specified with INPUT and INCLUDE_PATH.
# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
CLANG_OPTIONS =
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
# which the alphabetical index list will be split.
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 5
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefore more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET =
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the style sheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to YES can help to show when doxygen was last run and thus if the
# documentation is up to date.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = NO
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = NO
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see: http://developer.apple.com/tools/xcode/), introduced with
# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
# Makefile in the HTML output directory. Running make will produce the docset in
# that directory and running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
# Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler (hhc.exe). If non-empty,
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated
# (YES) or that it should be included in the master .chm file (NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated
# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = NO
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = org.doxygen.Project
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
# folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = doc
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location of Qt's
# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
# generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = NO
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 250
# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# http://www.mathjax.org) which uses client side Javascript for the rendering
# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from http://www.mathjax.org before deployment.
# The default value is: http://cdn.mathjax.org/mathjax/latest.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use + S
# (what the is depends on the OS and browser, but it is typically
# , /