initial commit

Author: rgc-tj

CMakeLists.txt

@@ -0,0 +1,256 @@
+cmake_minimum_required(VERSION 3.10)
+if (NOT CMAKE_CXX_COMPILER)
+  set(CMAKE_CXX_COMPILER g++)
+endif()
+
+execute_process(
+  COMMAND git log --pretty=format:%h -n 1
+  OUTPUT_VARIABLE GIT_COMMIT
+)
+if ("${GIT_COMMIT}" STREQUAL "")
+  set(GIT_COMMIT "NA")
+endif()
+
+file(STRINGS "VERSION" RM_VERSION)
+project(remeta VERSION ${RM_VERSION})
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+set(CMAKE_CXX_FLAGS "-O3 -Wall -ffast-math -fvisibility=hidden -fopenmp")
+add_definitions(-DVERSION_NUMBER="v${RM_VERSION}-${GIT_COMMIT}")
+
+add_executable(remeta
+  ${CMAKE_SOURCE_DIR}/src/io/bgz_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/bgz_writer.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/block_pgen_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/gene_set_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/htpv4_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/htpv4_writer.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/remeta_matrix_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/regenie_ld_matrix_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/regenie_ld_matrix_writer.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/ref_ld_block_mapper.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/ref_ld_genetic_map.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/ref_ld_matrix_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/ref_ld_matrix_writer.cpp
+  ${CMAKE_SOURCE_DIR}/src/io/regenie_anno_reader.cpp
+  ${CMAKE_SOURCE_DIR}/src/meta/es_meta_analyzer.cpp
+  ${CMAKE_SOURCE_DIR}/src/meta/genep_meta_analyzer.cpp
+  ${CMAKE_SOURCE_DIR}/src/meta/htp_meta_analyzer.cpp
+  ${CMAKE_SOURCE_DIR}/src/meta/pv_meta_analyzer.cpp
+  ${CMAKE_SOURCE_DIR}/src/meta/set_meta_analyzer.cpp
+  ${CMAKE_SOURCE_DIR}/src/meta/variant_meta_analyzer.cpp
+  ${CMAKE_SOURCE_DIR}/src/stat/misc.cpp
+  ${CMAKE_SOURCE_DIR}/src/stat/spa.cpp
+  ${CMAKE_SOURCE_DIR}/src/stat/tests.cpp
+  ${CMAKE_SOURCE_DIR}/src/allele_frequency_map.cpp
+  ${CMAKE_SOURCE_DIR}/src/annotation_map.cpp
+  ${CMAKE_SOURCE_DIR}/src/htpv4_pos.cpp
+  ${CMAKE_SOURCE_DIR}/src/logging.cpp
+  ${CMAKE_SOURCE_DIR}/src/parameter_checks.cpp
+  ${CMAKE_SOURCE_DIR}/src/remeta.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_acatv.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_compute_ref_ld.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_esma.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_genep.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_htp.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_index_anno.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_ld_deflate.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_ld_inflate.cpp
+  ${CMAKE_SOURCE_DIR}/src/run_pvma.cpp
+  ${CMAKE_SOURCE_DIR}/src/source_map.cpp
+  ${CMAKE_SOURCE_DIR}/src/util.cpp
+  ${CMAKE_SOURCE_DIR}/src/variant_filter.cpp
+)
+
+find_path(
+  EIGEN
+  Eigen
+  HINTS ${EIGEN_PATH}
+        /usr/local/include/eigen3
+)
+if (${EIGEN} STREQUAL EIGEN-NOTFOUND)
+  message(SEND_ERROR "could not find Eigen folder at EIGEN_PATH")
+else()
+  message("EIGEN: ${EIGEN}")
+endif()
+
+target_include_directories(remeta PRIVATE ${EIGEN})
+
+find_library(
+  HTSLIB
+  libhts.a
+  HINTS ${HTSLIB_PATH}
+)
+find_library(
+  DEFLATE
+  libdeflate.a
+)
+if (${HTSLIB} STREQUAL HTSLIB-NOTFOUND)
+  message(SEND_ERROR "Could not find libhts.a at ${HTSLIB_PATH}")
+else()
+  message("HTSlib: ${HTSLIB}")
+endif()
+if (${DEFLATE} STREQUAL DEFLATE-NOTFOUND)
+  message(SEND_ERROR "Could not find libdeflate.a")
+endif()
+
+find_library(
+  BOOST_LOG_SETUP
+  libboost_log_setup.a
+  HINTS ${BOOST_PATH}
+)
+find_library(
+  BOOST_LOG
+  libboost_log.a
+  HINTS ${BOOST_PATH}
+)
+find_library(
+  BOOST_PROGRAM_OPTIONS
+  libboost_program_options.a
+  HINTS ${BOOST_PATH}
+)
+find_library(
+  BOOST_FILESYSTEM
+  libboost_filesystem.a
+  HINTS ${BOOST_PATH}
+)
+find_library(
+  BOOST_SYSTEM
+  libboost_system.a
+  HINTS ${BOOST_PATH}
+)
+find_library(
+  BOOST_THREAD
+  libboost_thread.a
+  HINTS ${BOOST_PATH}
+)
+find_library(Z libz.so)
+find_library(SSL libssl.so)
+find_library(CRYPTO libcrypto.so)
+find_library(BZ2 libbz2.so)
+find_library(LZMA liblzma.so)
+find_library(CURL libcurl.so)
+
+set(EXTERNAL_LIBS
+  ${HTSLIB}
+  ${DEFLATE}
+  ${BOOST_LOG_SETUP}
+  ${BOOST_LOG}
+  ${BOOST_PROGRAM_OPTIONS}
+  ${BOOST_FILESYSTEM}
+  ${BOOST_SYSTEM}
+  ${BOOST_THREAD}
+  ${PTHREAD}
+  ${Z}
+  ${SSL}
+  ${CRYPTO}
+  ${DL}
+  ${BZ2}
+  ${LZMA}
+  ${CURL}
+)
+
+target_link_libraries(remeta PUBLIC ${EXTERNAL_LIBS})
+
+add_custom_target(
+  pgenlib.a
+  COMMAND make
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/lib/pgenlib
+)
+target_link_libraries(
+  remeta PUBLIC
+  ${CMAKE_SOURCE_DIR}/lib/pgenlib/pgenlib.a
+)
+target_include_directories(
+  remeta PUBLIC
+  ${CMAKE_SOURCE_DIR}/lib/pgenlib
+)
+add_dependencies(remeta pgenlib.a)
+
+add_custom_target(
+  faddeeva.a
+  COMMAND make
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/lib/faddeeva
+)
+target_link_libraries(
+  remeta PUBLIC
+  ${CMAKE_SOURCE_DIR}/lib/faddeeva/faddeeva.a
+)
+target_include_directories(
+  remeta PUBLIC
+  ${CMAKE_SOURCE_DIR}/lib/faddeeva
+)
+add_dependencies(remeta faddeeva.a)
+
+add_custom_target(
+  qfc.a
+  COMMAND make
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/lib/qfc
+)
+target_link_libraries(
+  remeta PUBLIC
+  ${CMAKE_SOURCE_DIR}/lib/qfc/qfc.a
+)
+target_include_directories(
+  remeta PUBLIC
+  ${CMAKE_SOURCE_DIR}/lib/qfc
+)
+add_dependencies(remeta qfc.a)
+
+#####################################
+### Link Linear Algebra Libraries ###
+#####################################
+# Intel MKL
+find_library(MKL libmkl_intel_lp64.a
+  HINTS ${MKLROOT} $ENV{MKLROOT}/lib
+)
+find_library(MKL_GNU_THREAD libmkl_gnu_thread.a
+  HINTS ${MKLROOT} $ENV{MKLROOT}/lib
+)
+find_library(MKL_CORE libmkl_core.a
+  HINTS ${MKLROOT} $ENV{MKLROOT}/lib
+)
+find_library(GOMP libgomp.a HINTS /usr/lib/gcc/x86_64-linux-gnu/8/)
+find_library(M NAMES m)
+
+# Openblas
+find_library(LAPACK liblapack.a)
+find_library(LAPACKE liblapacke.a)
+find_library(OPENBLAS libopenblas.a)
+
+if (MKL AND MKL_GNU_THREAD AND MKL_CORE)
+  message("Compiling with Intel MKL")
+  target_include_directories(remeta PRIVATE ${MKL_INCLUDE})
+  message("\t${MKL}")
+  message("\t${MKL_GNU_THREAD}")
+  message("\t${MKL_CORE}")
+  target_link_libraries(remeta PRIVATE
+    "-Wl,--start-group"
+    ${MKL} ${MKL_GNU_THREAD} ${MKL_CORE}
+    "-Wl,--end-group"
+    -lgomp
+    ${M}
+    -ldl)
+  #set(MKL_LINK static)
+  find_package(MKL CONFIG PATHS ${MKLROOT} $ENV{MKLROOT}} QUIET)
+  target_include_directories(remeta PRIVATE ${MKL_INCLUDE})
+  target_compile_definitions(remeta PUBLIC "-DMKL_ILP64 -DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE")
+elseif (LAPACK AND LAPACKE AND OPENBLAS)
+  message("Compiling with OpenBLAS")
+  message("\t${LAPACK}")
+  message("\t${LAPACKE}")
+  message("\t${OPENBLAS}")
+  set(BLAS_LIBS ${LAPACK} ${LAPACKE} ${OPENBLAS})
+
+  target_link_libraries(remeta PUBLIC ${BLAS_LIBS})
+  target_compile_definitions(remeta PUBLIC "-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE")
+else()
+  message("Missing libraries for Intel MKL and OpenBLAS")
+  message("\tLAPACK ${LAPACK}")
+  message("\tLAPACKE ${LAPACKE}")
+  message("\tOPENBLAS ${OPENBLAS}")
+  message("\tMKL ${MKL}")
+  message("\tMKL_GNU_THREAD ${MKL_GNU_THREAD}")
+  message("\tMKL_CORE ${MKL_CORE}")
+endif()

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Tyler Joseph, Joelle Mbatchou & Jonathan Marchini
+
+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.

README.md

@@ -0,0 +1,3 @@
+**remeta** is a collection of C++ programs for meta-analysis of single variants and gene-based tests using summary statistics from [**regenie**](https://rgcgithub.github.io/regenie/).
+
+Documentation for **remeta** can be found [here](https://rgcgithub.github.io/remeta/)

VERSION

@@ -0,0 +1 @@
+0.7.0

docker/remeta.dockerfile

@@ -0,0 +1,91 @@
+FROM ubuntu:22.04 as builder
+
+ENV CMAKE_VERSION 3.10
+ENV CMAKE_VERSION_PATCH 0
+ENV HTSLIB_VERSION 1.20
+ENV TMP_DIR /tmp
+
+COPY . ${TMP_DIR}/remeta
+
+ADD http://cmake.org/files/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}.${CMAKE_VERSION_PATCH}-Linux-x86_64.sh cmake_install.sh
+ADD https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB intel_key.PUB
+
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    g++ \
+    make \
+    gnupg \
+    gpg-agent \
+    wget \
+    bzip2 \
+    apt-transport-https \
+    ca-certificates \
+    git-all \
+    zlib1g-dev \
+    libboost-all-dev \
+    libz-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libgomp1 \
+    libdeflate-dev \
+    && sh -c 'cat intel_key.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null' \
+    && sh -c 'echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list' \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends intel-oneapi-mkl-devel \
+    && . /opt/intel/oneapi/setvars.sh \
+    && echo "MKL_THREADING_LAYER=GNU" >> /etc/environment \
+    && sh cmake_install.sh --prefix=/usr/local --skip-license --exclude-subdir \
+    && mkdir -p $TMP_DIR \
+    && wget -q --no-check-certificate https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2 \
+    && tar -xf eigen-3.4.0.tar.bz2 -C /usr/local/lib \
+    && rm eigen-3.4.0.tar.bz2 \
+    && wget -q --no-check-certificate https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/htslib-$HTSLIB_VERSION.tar.bz2 \
+    && tar -xf htslib-$HTSLIB_VERSION.tar.bz2 -C $TMP_DIR \
+    && rm htslib-$HTSLIB_VERSION.tar.bz2 \
+    && cd $TMP_DIR/htslib-$HTSLIB_VERSION/ \
+    && ./configure \
+    && make \
+    && make install \
+    && cp tabix /usr/local/bin/tabix \
+    && cd $TMP_DIR/remeta \
+    && rm -f CMakeCache.txt \
+    && cmake -D EIGEN_PATH=/usr/local/lib/eigen-3.4.0 \
+             -D CMAKE_CXX_COMPILER=g++ \
+             -D MKLROOT=${MKLROOT} \
+             . \
+    && make remeta \
+    && cp remeta /usr/local/bin/remeta \
+    && cd \
+    && rm -rf $TMP_DIR
+
+FROM ubuntu:22.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    g++ \
+    make \
+    gnupg \
+    wget \
+    apt-transport-https \
+    ca-certificates \
+    git-all \
+    zlib1g-dev \
+    libboost-all-dev \
+    libz-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libgomp1 \
+    libdeflate-dev
+
+COPY --from=builder /usr/local/bin/remeta /usr/local/bin/
+COPY --from=builder /usr/local/bin/tabix /usr/local/bin/

docs/cinder/404.html

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+{% extends "base.html" %}
+
+{% block content %}
+
+    <div class="row-fluid">
+      <div id="main-content" class="span12">
+        <h1 id="404-page-not-found" style="text-align: center">404</h1>
+        <p style="text-align: center"><strong>Page not found</strong></p>
+        <p style="text-align: center"><a href="{{ base_url }}">Home</a></p>
+      </div>
+    </div>
+
+{% endblock %}