Merge pull request #74 from DEploid-dev/68_new_version

68 new version

.Rbuildignore

@@ -2,7 +2,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.Rhistory$
-^tmp$
+^tmp.*
 ^NEWS\.md$
 
 # bash scripts

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.5.3
+Version: 0.5.4
 Authors@R: c(
     person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="[email protected]"),
-    person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
-    person('Gil', 'McVean', role=c('aut', 'cph')),
+    person('Jacob', 'Almagro-Garcia', role=c('aut')),
+    person('Gil', 'McVean', role=c('aut')),
     person('University of Oxford', '', role=c('cph')),
     person('Yinghan', 'Liu', role=c('ctb')),
     person('CodeCogs', 'Zyba Ltd', role=c('com', "cph")),
@@ -37,8 +37,8 @@ Imports:
 Suggests:
     knitr,
     testthat (>= 0.9.0)
-SystemRequirements: C++11
 VignetteBuilder: knitr
 LinkingTo: Rcpp
-RoxygenNote: 7.1.0
-Date: 2020-04-21
+RoxygenNote: 7.3.2
+Encoding: UTF-8
+Date: 2024-10-8

NAMESPACE

@@ -1,26 +1,37 @@
-importFrom("scales", "alpha")
-importFrom("grDevices", "rainbow", "colorRampPalette")
-importFrom("graphics", "abline", "barplot", "hist", "plot", "points", "axis", "legend")
-importFrom("utils", "read.table")
-importFrom(Rcpp,evalCpp)
-importFrom("magrittr", "%>%")
-importFrom("plotly", "plot_ly", "layout", "add_trace")
-importFrom("rmarkdown", "pandoc_available")
-importFrom("htmlwidgets", "saveWidget")
-useDynLib(DEploid, .registration = TRUE)
+# Generated by roxygen2: do not edit by hand
+
+export(computeObsWSAF)
 export(dEploid)
-export(extractVcf)
-export(plotProportions)
-export(extractCoverageFromVcf)
 export(extractCoverageFromTxt)
+export(extractCoverageFromVcf)
+export(extractPLAF)
+export(extractVcf)
 export(haplotypePainter)
-export(plotAltVsRef)
-export(computeObsWSAF)
 export(histWSAF)
-export(extractPLAF)
-export(plotWSAFvsPLAF)
-export(plotObsExpWSAF)
+export(plotAltVsRef)
 export(plotAltVsRefPlotly)
 export(plotHistWSAFPlotly)
-export(plotWSAFVsPLAFPlotly)
+export(plotObsExpWSAF)
 export(plotObsExpWSAFPlotly)
+export(plotProportions)
+export(plotWSAFVsPLAFPlotly)
+export(plotWSAFvsPLAF)
+importFrom(Rcpp,evalCpp)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,rainbow)
+importFrom(graphics,abline)
+importFrom(graphics,axis)
+importFrom(graphics,barplot)
+importFrom(graphics,hist)
+importFrom(graphics,legend)
+importFrom(graphics,plot)
+importFrom(graphics,points)
+importFrom(htmlwidgets,saveWidget)
+importFrom(magrittr,"%>%")
+importFrom(plotly,add_trace)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)
+importFrom(rmarkdown,pandoc_available)
+importFrom(scales,alpha)
+importFrom(utils,read.table)
+useDynLib(DEploid, .registration = TRUE)

R/dEploid.R

@@ -1,3 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
 #' Deconvolute Mixed Genomes with Unknown Proportions
 #'
 #' Traditional phasing programs are limited to diploid organisms.
@@ -18,9 +21,16 @@
 #' Maintainer: Joe Zhu \email{[email protected]}
 #'
 #' @name DEploid-package
-#' @docType package
 #'
 #' @importFrom Rcpp evalCpp
-#' @useDynLib _DEploid_dEploid
-#' @useDynLib _DEploid_extractVcf
+#' @importFrom scales alpha
+#' @importFrom grDevices rainbow colorRampPalette
+#' @importFrom graphics abline barplot hist plot points axis legend
+#' @importFrom utils read.table
+#' @importFrom magrittr %>%
+#' @importFrom plotly plot_ly layout add_trace
+#' @importFrom rmarkdown pandoc_available
+#' @importFrom htmlwidgets saveWidget
+#' @useDynLib DEploid, .registration = TRUE
 NULL
+

README.md

@@ -1,10 +1,10 @@
 <img src="inst/extdata/deploid.png" width="180">
 
 [![License (GPL version 3)](https://img.shields.io/badge/license-GPL%20version%203-brightgreen.svg)](http://opensource.org/licenses/GPL-3.0)
-[![Build Status](https://travis-ci.org/DEploid-dev/DEploid-r.svg?branch=master)](https://travis-ci.org/DEploid-dev/DEploid-r)
+[![Build Status](https://travis-ci.org/DEploid-dev/DEploid-r.svg?branch=master)](https://app.travis-ci.com/DEploid-dev/DEploid-r)
 [![Build Status](https://ci.appveyor.com/api/projects/status/hi1nq97d5l68qs4r?svg=true)](https://ci.appveyor.com/project/shajoezhu/deploid-r)
 [![Coverage Status](https://coveralls.io/repos/github/DEploid-dev/DEploid-r/badge.svg?branch=master)](https://coveralls.io/github/DEploid-dev/DEploid-r?branch=master)
-[![codecov](https://codecov.io/gh/DEploid-dev/DEploid-r/branch/master/graph/badge.svg)](https://codecov.io/gh/DEploid-dev/DEploid-r)
+[![codecov](https://codecov.io/gh/DEploid-dev/DEploid-r/branch/master/graph/badge.svg)](https://app.codecov.io/gh/DEploid-dev/DEploid-r)
 [![CRAN RStudio Mirror Downloads](http://cranlogs.r-pkg.org/badges/DEploid)](https://cran.r-project.org/package=DEploid)
 
 DEploid R package -- Deconvolute Mixed Genomes with Unknown Proportions

inst/CITATION

@@ -8,5 +8,5 @@ bibentry(
   journal = 'bioRxiv',
   doi = '10.1101/099499',
   publisher = 'Cold Spring Harbor Labs Journals',
-  url = 'http://www.biorxiv.org/content/early/2017/01/10/099499'
+  url = 'https://www.biorxiv.org/content/10.1101/099499v1'
 )

src/DEploid/dEploidIO.cpp

@@ -190,7 +190,7 @@ void DEploidIO::reInit() {
 
 
 void DEploidIO::finalize() {
-    if ( this->doIbdPainting() | this->doComputeLLK() | this->doIbdViterbiPainting() ) {
+    if ( this->doIbdPainting() || this->doComputeLLK() || this->doIbdViterbiPainting() ) {
         if (!initialPropWasGiven()) {
             throw InitialPropUngiven("");
         }
@@ -541,7 +541,7 @@ void DEploidIO::checkInput() {
             // set k strain by proportion length
         }
     }
-    if (this->useBestPractice() & (!this->usePanel())){
+    if (this->useBestPractice() && (!this->usePanel())){
         throw FlagsConflict("-best" , string("-noPanel. Reference panel is") +
             string("required for using best-practices."));
     }
@@ -764,7 +764,7 @@ void DEploidIO::readPanel() {
     if ( this->usePanel() == false ) {
         return;
     }
-    if ( this->doIbdPainting() | this->doComputeLLK() ) {
+    if ( this->doIbdPainting() || this->doComputeLLK() ) {
         return;
     }
 

src/DEploid/exceptions.hpp

@@ -39,7 +39,8 @@ struct ShouldNotBeCalled : std::exception{
   ShouldNotBeCalled() { }
   virtual ~ShouldNotBeCalled() throw() {}
   virtual const char* what() const noexcept {
-      return string("Should not reach here").c_str();
+      static const std::string msg = "Should not reach here";
+      return msg.c_str();
   }
 };
 
@@ -75,7 +76,8 @@ struct OutOfVectorSize : std::exception{
   OutOfVectorSize() { }
   virtual ~OutOfVectorSize() throw() {}
   virtual const char* what() const noexcept {
-      return string("Out of vector size!").c_str();
+      static const std::string msg = "Out of vector size!";
+      return msg.c_str();
   }
 };
 

src/DEploid/mcmc.cpp

@@ -314,7 +314,7 @@ void McmcMachinery::runMcmcChain( bool showProgress, bool useIBD, bool notInR )
         this->mcmcSample_->siteOfOneMissCopyOne[atSiteI] /= (double)this->maxIteration_;
     }
 
-    if ( notInR & ((jobbrief == "lassoK") | (jobbrief == "ibd") | (jobbrief == "classic")) ) { // notInPython
+    if ( notInR & ((jobbrief == "lassoK") || (jobbrief == "ibd") || (jobbrief == "classic")) ) { // notInPython
         this->dEploidIO_->writeMcmcRelated(this->mcmcSample_, jobbrief, useIBD);
     }
 

src/DEploid/random/fastfunc.hpp

@@ -29,6 +29,7 @@
 #include <iostream>
 #include <cmath>
 #include <vector>
+#include <cstdint>
 
 
 // Number of interpolation points.  If this is changed, several constants in fastlog must also be changed.
@@ -85,8 +86,8 @@ inline double FastFunc::fastexp_lo(double y) {
 
 inline double FastFunc::fastlog(double x) {
   const float offset = 2047;                // as int64_t: 0x409ffc00000....
-  double y = x;
-  int64_t* yint = (int64_t*)(&y);
+  //double y = x;   int64_t* yint = reinterpret_cast<int64_t*>(&y);
+  int64_t* yint = reinterpret_cast<int64_t*>(&x);
   int expon = ((*yint) >> 52) - 1023;       // base-2 exponent of float
   int index = ((*yint) >> (52-10)) & 1023;  // upper 10 bits of mantissa
   *yint |= 0x7ffffc0000000000;              // convert float into remainder of mantissa; and

src/Makevars.win

@@ -23,6 +23,5 @@ OBJECTS.dEploid = DEploid/dEploidIO.o \
 
 
 OBJECTS = $(OBJECTS.dEploidr) $(OBJECTS.dEploid)
-CXX_STD = CXX11
 PKG_CXXFLAGS = -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS
 PKG_LIBS = -lz

src/RcppExports.cpp

@@ -5,6 +5,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // dEploid
 List dEploid(std::string args);
 RcppExport SEXP _DEploid_dEploid(SEXP argsSEXP) {

src/init.c

@@ -10,9 +10,9 @@
 /* .Call calls */
 extern SEXP _DEploid_dEploid(SEXP);
 extern SEXP _DEploid_extractVcf(SEXP);
-extern SEXP _DEploid_test_RRG_sample();
+extern SEXP _DEploid_test_RRG_sample(void);
 extern SEXP _DEploid_test_RRG_sampleExpoExpoLimit(SEXP, SEXP, SEXP);
-extern SEXP _DEploid_test_RRG_sampleUnitExpo();
+extern SEXP _DEploid_test_RRG_sampleUnitExpo(void);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_DEploid_dEploid",                      (DL_FUNC) &_DEploid_dEploid,                      1},

vignettes/dEploid-Arguments.Rmd

@@ -198,8 +198,8 @@ Bibtex record::
   year = {2018},
   doi = {10.1101/387266},
   publisher = {Cold Spring Harbor Laboratory},
-  URL = {https://www.biorxiv.org/content/early/2018/08/09/387266},
-  eprint = {https://www.biorxiv.org/content/early/2018/08/09/387266.full.pdf},
+  URL = {https://www.biorxiv.org/content/10.1101/387266v1},
+  eprint = {https://www.biorxiv.org/content/biorxiv/early/2018/08/09/387266.full.pdf},
   journal = {bioRxiv}
   }