Merge 7bef150 into 0d5e42c

DEploid-dev · Apr 17, 2020 · 3b5fad6 · 3b5fad6
2 parents 0d5e42c + 7bef150
commit 3b5fad6
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Showing 15 changed files with 16 additions and 155 deletions.
diff --git a/.DEploid b/.DEploid
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,6 +14,7 @@
 ^\.travis\.yml$
 ^appveyor\.yml$
 ^\.lintr$
+lint-and-covr.Rout
 
 # C++
 \.o$
@@ -25,7 +26,10 @@
 src/DEploid/dEploid.cpp
 src/DEploid/lasso/lassoOut.cpp
 src/DEploid/gzstream/version
+src/DEploid/export/mcmcIO.cpp
+src/DEploid/gzstream/version
 src/DEploid/lasso/.ci/
+src/DEploid/lasso/.git
 src/DEploid/lasso/.gitignore
 src/DEploid/lasso/.travis.yml
 src/DEploid/lasso/Brewfile

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,7 +9,6 @@ importFrom("rmarkdown", "pandoc_available")
 importFrom("htmlwidgets", "saveWidget")
 useDynLib(DEploid, .registration = TRUE)
 export(dEploid)
-export(extractVcf)
 export(plotProportions)
 export(extractCoverageFromVcf)
 export(extractCoverageFromTxt)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -40,36 +40,6 @@ dEploid <- function(args) {
     .Call(`_DEploid_dEploid`, args)
 }
 
-#' @title Extract VCF information
-#'
-#' @description Extract VCF information
-#'
-#' @param filename VCF file name.
-#'
-#' @seealso
-#' \itemize{
-#'   \item \code{extractCoverageFromVcf}
-#'   \item \code{extractCoverageFromTxt}
-#' }
-#'
-#' @return A dataframe list with members of haplotypes, proportions and log likelihood of the MCMC chain.
-#' \itemize{
-#'   \item \code{CHROM} SNP chromosomes.
-#'   \item \code{POS} SNP positions.
-#'   \item \code{refCount} reference allele count.
-#'   \item \code{altCount} alternative allele count.
-#' }
-#'
-#' @export
-#'
-#' @examples
-#' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
-#' vcf = extractVcf(vcfFile)
-#'
-extractVcf <- function(filename) {
-    .Call(`_DEploid_extractVcf`, filename)
-}
-
 test_RRG_sample <- function() {
     .Call(`_DEploid_test_RRG_sample`)
 }

diff --git a/R/dEploid.R b/R/dEploid.R
@@ -22,5 +22,4 @@
 #'
 #' @importFrom Rcpp evalCpp
 #' @useDynLib _DEploid_dEploid
-#' @useDynLib _DEploid_extractVcf
 NULL
diff --git a/cpHardCopies.sh b/cpHardCopies.sh
@@ -8,9 +8,14 @@ rsync -avu R/DEploidR.R .DEploid/utilities/DEploidR.R
 #rsync -avu src/DEploid/ .DEploid/src/
 
 # sync from DEploid to DEploid-r
-rsync -avu .DEploid/src/ src/DEploid/
+rsync -avu .DEploid/src/*pp src/DEploid/
+rsync -avu .DEploid/src/codeCogs/ src/DEploid/codeCogs/
+rsync -avu .DEploid/src/debug/ src/DEploid/debug/
+rsync -avu .DEploid/src/export/ src/DEploid/export/
+rsync -avu .DEploid/src/gzstream/ src/DEploid/gzstream/
+rsync -avu .DEploid/src/random/ src/DEploid/random/
 rsync -avu .DEploid/src/lasso/*pp src/DEploid/lasso/
-#cp .DEploid/DEploid-Lasso-lib/src/*pp lasso
+rsync -avu .DEploid/src/lasso/*pp src/DEploid/lasso/src/
 
 # tidy up
 #rm -r src/DEploid/*/.deps

diff --git a/man/extractVcf.Rd b/man/extractVcf.Rd
diff --git a/src/DEploid/gzstream/gzstream.h b/src/DEploid/gzstream/gzstream.h
@@ -28,7 +28,6 @@
 
 #ifndef GZSTREAM_H
 #define GZSTREAM_H 1
-#define ZLIB_WINAPI
 
 // standard C++ with new header file names and std:: namespace
 #include <iostream>
@@ -119,4 +118,3 @@ class ogzstream : public gzstreambase, public std::ostream {
 #endif // GZSTREAM_H
 // ============================================================================
 // EOF //
-
diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,4 +1,4 @@
-OBJECTS.dEploidr = rvcf.o dEploidr.o test_exports.o RcppExports.o init.o
+OBJECTS.dEploidr = dEploidr.o test_exports.o RcppExports.o init.o
 
 OBJECTS.dEploid = DEploid/dEploidIO.o \
     DEploid/ibd.o \

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -16,17 +16,6 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// extractVcf
-Rcpp::DataFrame extractVcf(std::string filename);
-RcppExport SEXP _DEploid_extractVcf(SEXP filenameSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< std::string >::type filename(filenameSEXP);
-    rcpp_result_gen = Rcpp::wrap(extractVcf(filename));
-    return rcpp_result_gen;
-END_RCPP
-}
 // test_RRG_sample
 double test_RRG_sample();
 RcppExport SEXP _DEploid_test_RRG_sample() {

diff --git a/src/dEploidr.cpp b/src/dEploidr.cpp
@@ -23,6 +23,7 @@
  *
  */
 
+#define STRICT_R_HEADERS
 #include <Rcpp.h>
 #include <iostream> // std::cout
 #include "mcmc.hpp"

diff --git a/src/init.c b/src/init.c
@@ -9,14 +9,12 @@
 
 /* .Call calls */
 extern SEXP _DEploid_dEploid(SEXP);
-extern SEXP _DEploid_extractVcf(SEXP);
 extern SEXP _DEploid_test_RRG_sample();
 extern SEXP _DEploid_test_RRG_sampleExpoExpoLimit(SEXP, SEXP, SEXP);
 extern SEXP _DEploid_test_RRG_sampleUnitExpo();
 
 static const R_CallMethodDef CallEntries[] = {
     {"_DEploid_dEploid",                      (DL_FUNC) &_DEploid_dEploid,                      1},
-    {"_DEploid_extractVcf",                   (DL_FUNC) &_DEploid_extractVcf,                   1},
     {"_DEploid_test_RRG_sample",              (DL_FUNC) &_DEploid_test_RRG_sample,              0},
     {"_DEploid_test_RRG_sampleExpoExpoLimit", (DL_FUNC) &_DEploid_test_RRG_sampleExpoExpoLimit, 3},
     {"_DEploid_test_RRG_sampleUnitExpo",      (DL_FUNC) &_DEploid_test_RRG_sampleUnitExpo,      0},

diff --git a/src/r_random_generator.h b/src/r_random_generator.h
@@ -27,6 +27,7 @@
 #ifndef dEploidr_r_random_generator
 #define dEploidr_r_random_generator
 
+#define STRICT_R_HEADERS
 #include <Rcpp.h>
 #include <memory>
 #include "random_generator.hpp"

diff --git a/src/rvcf.cpp b/src/rvcf.cpp
diff --git a/src/test_exports.cpp b/src/test_exports.cpp
@@ -1,3 +1,4 @@
+#define STRICT_R_HEADERS
 #include <Rcpp.h>
 #include <memory>