Merge branch 'build-test'

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.1)
+cmake_minimum_required(VERSION 3.1)
 
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Release)
@@ -7,13 +7,19 @@ endif()
 set(PROJECT_NAME PRSice)
 project(${PROJECT_NAME})
 set(CMAKE_CXX_FLAGS "-g -Wall")
-
+include(CheckCXXCompilerFlag)
+CHECK_CXX_COMPILER_FLAG("-std=c++17" COMPILER_SUPPORTS_CXX17)
+if(COMPILER_SUPPORTS_CXX17)
+    message(STATUS "${COMPILER_SUPPORTS_CXX17}")
+else(COMPILER_SUPPORTS_CXX17)
+    message(FATAL_ERROR "${COMPILER_SUPPORTS_CXX17}")
+endif(COMPILER_SUPPORTS_CXX17)
 option(march "Use --march." OFF)
 if(march)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
 endif()
 # Use C++11
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 # Require (at least) it
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 # Don't use e.g. GNU extension (like -std=gnu++11) for portability

PRSice.R

@@ -19,7 +19,7 @@ In_Regression <-
     R2 <-
     print.p <- R <- P <- value <- Phenotype <- Set <- PRS.R2 <- LCI <- UCI <- quant.ref <- NULL
 
-r.version <- "2.2.12"
+r.version <- "2.2.13"
 # Help Messages --------------------------------------
 help_message <-
 "usage: Rscript PRSice.R [options] <-b base_file> <-t target_file> <--prsice prsice_location>\n
@@ -298,7 +298,7 @@ help_message <-
     --keep-ambig            Keep ambiguous SNPs. Only use this option\n
                             if you are certain that the base and target\n
                             has the same A1 and A2 alleles\n
-    --keep-ambig-as-is      Will not flip ambiguous SNPs when they are kept.\n
+    --flip-ambig            Force flipping of ambiguous SNPs when they are kept.\n
                             Will also set the --keep-ambig flag\n
     --id-delim              This parameter causes sample IDs to be parsed as\n
                             <FID><delimiter><IID>; the default delimiter\n
@@ -541,7 +541,7 @@ option_list <- list(
   make_option(c("--id-delim"), type = "character"), 
   make_option(c("--logit-perm"), action = "store_true", dest = "logit_perm"),
   make_option(c("--keep-ambig"), action = "store_true", dest = "keep_ambig"),
-  make_option(c("--keep-ambig-as-is"), action = "store_true", dest = "keep_ambig_as_is"),
+  make_option(c("--flip-ambig"), action = "store_true", dest = "flip_ambig"),
   make_option(c("--memory"), type = "character", dest="memory"),
   make_option(c("-o", "--out"), type = "character", default = "PRSice"),
   make_option(c("--perm"), type = "numeric"),
@@ -691,7 +691,7 @@ flags <-
         "ignore-fid",
         "index",
         "keep-ambig",
-        "keep-ambig-as-is",
+        "flip-ambig",
         "logit-perm",
         "no-clump",
         "no-default",

Release/packing.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+rm *.zip
 zip PRSice_linux.zip PRSice.R TOY* PRSice_linux
 zip PRSice_mac.zip PRSice.R TOY* PRSice_mac
 zip PRSice_win64.zip PRSice.R TOY* PRSice_win64.exe

helpers/help_messages.txt

@@ -2,23 +2,23 @@ m_help_message =
        "usage: PRSice [options] <-b base_file> <-t target_file>\n"
            // Base file
        "\nBase File:\n"
-       "    --A1                    Column header containing allele 1 (effective allele)\n"
+       "    --a1                    Column header containing allele 1 (effective allele)\n"
        "                            Default: A1\n"
-       "    --A2                    Column header containing allele 2 (non-effective allele)\n"
+       "    --a2                    Column header containing allele 2 (non-effective allele)\n"
        "                            Default: A2\n"
        "    --base          | -b    Base association file\n"
        "    --base-info             Base INFO score filtering. Format should be\n"
-       "                            <Column name>,<Threshold>. SNPs with info \n"
+       "                            <Column name>:<Threshold>. SNPs with info \n"
        "                            score less than <Threshold> will be ignored\n"
        "                            Column name default: INFO\n"
        "                            Threshold default: 0.9\n"
        "    --base-maf             Base MAF filtering. Format should be\n"
-       "                            <Column name>,<Threshold>. SNPs with maf\n"
+       "                            <Column name>:<Threshold>. SNPs with maf\n"
        "                            less than <Threshold> will be ignored. An\n"
        "                            additional column can also be added (e.g.\n"
        "                            also filter MAF for cases), using the\n"
        "                            following format:\n"
-       "                            <Column name>,<Threshold>:<Column name>,<Threshold>\n"
+       "                            <Column name>:<Threshold>,<Column name>:<Threshold>\n"
        "    --beta                  Whether the test statistic is in the form of \n"
        "                            BETA or OR. If set, test statistic is assume\n"
        "                            to be in the form of BETA. Mutually exclusive\n"
@@ -259,8 +259,6 @@ m_help_message =
        "    --keep-ambig            Keep ambiguous SNPs. Only use this option\n"
        "                            if you are certain that the base and target\n"
        "                            has the same A1 and A2 alleles\n"
-       "    --keep-ambig-as-is      Will not flip ambiguous SNPs when they are kept.\n"
-       "                            Will also set the --keep-ambig flag\n"
        "    --logit-perm            When performing permutation, still use logistic\n"
        "                            regression instead of linear regression. This\n"
        "                            will substantially slow down PRSice\n"