Release 4.15.0

.gitignore

@@ -1,4 +1,36 @@
-raremetal/obj/
-raremetalworker/obj/
-bin/raremetalworkerTest
-bin/raremetalTest
+# Build process artifacts
+cget/
+build*
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+#Jetbrains
+.idea/

CMakeLists.txt

@@ -0,0 +1,143 @@
+cmake_minimum_required(VERSION 3.2)
+project(raremetal VERSION 4.15.0 LANGUAGES C CXX Fortran)
+
+set(CMAKE_CXX_STANDARD 11)
+
+find_package(Threads)
+find_library(LIB_STATGEN StatGen)
+find_library(LIB_SAVVY savvy)
+find_library(LIB_ZSTD zstd)
+find_library(LIB_HTS hts)
+find_library(LIB_Z z)
+find_library(LIB_RMATH Rmath)
+
+add_library(libraremetal
+            libRareMetal/mvtnorm/randomF77.c
+            libRareMetal/pdf/PDF.cpp
+            libRareMetal/pdf/PDF.h
+            libRareMetal/pdf/PDFchartaxis.cpp
+            libRareMetal/pdf/PDFchartaxis.h
+            libRareMetal/pdf/PDFchartbar.cpp
+            libRareMetal/pdf/PDFchartbar.h
+            libRareMetal/pdf/PDFchartbasics.cpp
+            libRareMetal/pdf/PDFchartbasics.h
+            libRareMetal/pdf/PDFchartlegend.cpp
+            libRareMetal/pdf/PDFchartlegend.h
+            libRareMetal/pdf/PDFchartline.cpp
+            libRareMetal/pdf/PDFchartline.h
+            libRareMetal/pdf/PDFchartmarker.cpp
+            libRareMetal/pdf/PDFchartmarker.h
+            libRareMetal/pdf/PDFchartobject.cpp
+            libRareMetal/pdf/PDFchartobject.h
+            libRareMetal/pdf/PDFfont.cpp
+            libRareMetal/pdf/PDFfont.h
+            libRareMetal/pdf/PDFgrid.cpp
+            libRareMetal/pdf/PDFgrid.h
+            libRareMetal/pdf/PDFgridcell.cpp
+            libRareMetal/pdf/PDFgridcell.h
+            libRareMetal/pdf/PDFhistogram.cpp
+            libRareMetal/pdf/PDFhistogram.h
+            libRareMetal/pdf/PDFinfo.cpp
+            libRareMetal/pdf/PDFinfo.h
+            libRareMetal/pdf/PDFlinechart.cpp
+            libRareMetal/pdf/PDFlinechart.h
+            libRareMetal/pdf/PDFlinechartwithpolygon.cpp
+            libRareMetal/pdf/PDFlinechartwithpolygon.h
+            libRareMetal/pdf/PDFmanhattan.cpp
+            libRareMetal/pdf/PDFmanhattan.h
+            libRareMetal/pdf/PDFpage.cpp
+            libRareMetal/pdf/PDFpage.h
+            libRareMetal/pdf/PDFpageobject.cpp
+            libRareMetal/pdf/PDFpageobject.h
+            libRareMetal/src/Kinship.cpp
+            libRareMetal/src/Kinship.h
+            libRareMetal/src/KinshipX.cpp
+            libRareMetal/src/KinshipX.h
+            libRareMetal/src/MathCholesky.cpp
+            libRareMetal/src/MathCholesky.h
+            libRareMetal/src/MathDeriv.cpp
+            libRareMetal/src/MathDeriv.h
+            libRareMetal/src/MathFloatVector.cpp
+            libRareMetal/src/MathFloatVector.h
+            libRareMetal/src/MathGenMin.cpp
+            libRareMetal/src/MathGenMin.h
+            libRareMetal/src/MathGold.cpp
+            libRareMetal/src/MathGold.h
+            libRareMetal/src/MathNormal.cpp
+            libRareMetal/src/MathNormal.h
+            libRareMetal/src/MathSVD.cpp
+            libRareMetal/src/MathSVD.h
+            libRareMetal/src/Rmath.h
+            libRareMetal/src/TraitTransformations.cpp
+            libRareMetal/src/TraitTransformations.h
+            libRareMetal/mvtnorm/mvt.f)
+
+set_target_properties(libraremetal PROPERTIES OUTPUT_NAME raremetal)
+target_include_directories(libraremetal PUBLIC libRareMetal/pdf libRareMetal/src)
+target_link_libraries(libraremetal ${LIB_STATGEN} ${LIB_HTS} ${CMAKE_THREAD_LIBS_INIT} ${LIB_Z} ${LIB_RMATH})
+
+add_executable(raremetal
+#               raremetal/src/Calculate_mvt_pvalue.h
+#               raremetal/src/group.cpp
+               raremetal/src/GroupFromAnnotation.cpp
+               raremetal/src/GroupFromAnnotation.h
+               raremetal/src/Main.cpp
+               raremetal/src/Meta.cpp
+               raremetal/src/Meta.h
+               raremetal/src/MetaUtility.cpp
+               raremetal/src/MetaUtility.h
+#               raremetal/src/MixChidist.h
+#               raremetal/src/My_mvt.h
+#               raremetal/src/qfc.h
+               raremetal/src/QuadProg.cpp
+               raremetal/src/QuadProg.h
+#               raremetal/src/Rmath.h
+               raremetal/src/SummaryFileReader.cpp
+               raremetal/src/SummaryFileReader.h
+#               raremetal/src/WriteLog.h
+               raremetal/src/WritePDF.cpp
+               raremetal/src/WritePDF.h)
+
+target_include_directories(raremetal PRIVATE otherLib/eigen-3.2.0)
+target_link_libraries(raremetal libraremetal)
+target_compile_definitions(raremetal PRIVATE VERSION="${PROJECT_VERSION}")
+
+add_executable(raremetalworker
+               raremetalworker/src/AutoFit.cpp
+               raremetalworker/src/AutoFit.h
+               raremetalworker/src/AutoFit2.cpp
+               raremetalworker/src/AutoFit2.h
+               #raremetalworker/src/CheckRef.cpp
+               #raremetalworker/src/CheckRef.h
+               raremetalworker/src/DataQC.cpp
+               raremetalworker/src/DataQC.h
+               raremetalworker/src/FastFit.cpp
+               raremetalworker/src/FastFit.h
+               raremetalworker/src/GroupFromAnnotation.cpp
+               raremetalworker/src/GroupFromAnnotation.h
+               raremetalworker/src/KinshipEmp.cpp
+               raremetalworker/src/KinshipEmp.h
+               raremetalworker/src/logistic.cpp
+               raremetalworker/src/logistic.h
+               raremetalworker/src/Main.cpp
+               raremetalworker/src/OutputKin.cpp
+               raremetalworker/src/OutputKin.h
+               raremetalworker/src/PreMeta.cpp
+               raremetalworker/src/PreMeta.h
+               #raremetalworker/src/Rmath.h
+               #raremetalworker/src/snpHWE.h
+               raremetalworker/src/TransformResiduals.cpp
+               raremetalworker/src/TransformResiduals.h
+               #raremetalworker/src/WriteLog.h
+               raremetalworker/src/WritePDF.cpp
+               raremetalworker/src/WritePDF.h)
+
+target_include_directories(raremetalworker PRIVATE otherLib/eigen-3.2.0)
+target_link_libraries(raremetalworker libraremetal ${LIB_SAVVY} ${LIB_ZSTD})
+target_compile_definitions(raremetalworker PRIVATE VERSION="${PROJECT_VERSION}")
+
+
+if(BUILD_TESTS)
+    enable_testing()
+    add_subdirectory(tests)
+endif()

README.md

@@ -1,18 +1,51 @@
 Raremetal: A tool for rare variants meta-analysis
 
-(c) 2012-2017 Shuang Feng, Dajiang Liu, Sai Chen, Gonçalo Abecasis
+(c) 2012-2019 Shuang Feng, Dajiang Liu, Sai Chen, Gonçalo Abecasis
 
-For more info, please see wiki page
-http://genome.sph.umich.edu/wiki/RAREMETAL
+For more information, please see the [RAREMETAL wiki](http://genome.sph.umich.edu/wiki/RAREMETAL).
 
+## Installation
+1. Clone this repository
+2. Open a terminal and change to the directory containing this README file.
+3. Enter the following sequence of commands to download dependencies and build the code:
+
+```bash
+$ cget install -f requirements.txt
+$ mkdir build && cd build
+$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DBUILD_TESTS=1 ..
+$ make
+```
 
-**There is a known issue with the newest versions (>=4.14.0) of RAREMETAL, which may give incorrect p-values for some
- burden test calculation methods. We are working on a fix, but for now we recommend using an older version (<= 4.13.9).**
+To run unit tests, ensure that you have run cmake with `-DBUILD_TESTS=1` and built at least once, 
+then run `make` or `ctest --verbose`. These unit tests were written on Mac OS and you may encounter small differences 
+due to system precision on other platforms.
 
+If you encounter problems while building, see the [wiki instructions](https://genome.sph.umich.edu/wiki/RAREMETAL_DOWNLOAD_%26_BUILD) 
+and [FAQ](https://genome.sph.umich.edu/wiki/RAREMETAL_FAQ) for more information.
 
-Newest version: v.4.14.1 released at 07/10/2017
-- Some bug fixes
-- View change log at: http://genome.sph.umich.edu/wiki/RAREMETAL_Change_Log
+### Requirements
+Raremetal requires the following libraries to build. These should already be installed on most scientific 
+computing clusters.
 
-We've made a brand new version, RAREMETAL2. Still in beta, but a full release is planned in the future. See:
+- libRMath (The R math library. If not installed, use `apt-get install r-mathlib` on ubuntu or `brew install r` 
+    on Mac OS)
+- zlib (`apt-get install zlib1g-dev` on Ubuntu)
+
+### Troubleshooting
+On Mac OS, installing R as a standalone package is not sufficient to use libRMath in other executables. 
+Consider `brew install r` or [r-devel](https://r.research.att.com/) in that case.   
+
+On Mac OS, some `cget` dependencies (such as xz) may fail to install. In certain cases, this can be fixed by running an 
+OS-version-specific command similar to the below:
+
+`$ open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg`
+
+## Changes
+Newest version: v4.15.0 released March 14, 2019.
+View change log at: http://genome.sph.umich.edu/wiki/RAREMETAL_Change_Log
+
+### RAREMETAL2
+We are also working on a beta version that provides new features and options- RAREMETAL2. 
+
+This code is still in the experimental stages, but a full release is planned in the future. See:
 https://github.com/statgen/Raremetal2

dep/libstatgen.cmake

@@ -0,0 +1,15 @@
+cmake_minimum_required(VERSION 3.2)
+project(libStatGen VERSION 1.0.0)
+
+#execute_process(COMMAND ./configure --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+
+add_custom_target(libStatGen ALL COMMAND make CFLAGS="\"--std=c++11 -I${CMAKE_PREFIX_PATH}/include ${CMAKE_CXX_FLAGS}\"" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMENT "Building libStatGen ...")
+
+file(GLOB_RECURSE LSG_HEADER_LIST "bam/*.h" "fastq/*.h" "general/*.h" "glf/*.h" "vcf/*.h")
+install(FILES ${LSG_HEADER_LIST} DESTINATION include)
+
+if (BUILD_SHARED_LIBS)
+    install(FILES ${CMAKE_SHARED_LIBRARY_PREFIX}StatGen${CMAKE_SHARED_LIBRARY_SUFFIX} DESTINATION lib)
+else()
+    install(FILES ${CMAKE_STATIC_LIBRARY_PREFIX}StatGen${CMAKE_STATIC_LIBRARY_SUFFIX} DESTINATION lib)
+endif()

dep/rmath.cmake

@@ -0,0 +1,7 @@
+cmake_minimum_required(VERSION 3.2)
+project(libRmath VERSION 1.0.0)
+
+add_custom_target(libRmath ALL COMMAND make CFLAGS="\"-I${CMAKE_PREFIX_PATH}/include ${CMAKE_CXX_FLAGS}\"" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMENT "Building libRmath ...")
+
+install(DIRECTORY Rmath DESTINATION include)
+install(FILES ${CMAKE_STATIC_LIBRARY_PREFIX}Rmath${CMAKE_STATIC_LIBRARY_SUFFIX} DESTINATION lib)