bump version to 0.5.0

Author: shajoezhu

.DEploid

@@ -1,7 +1,7 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.4.4
+Version: 0.5.0
 Authors@R: c(
     person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="joe.zhu@well.ox.ac.uk"),
     person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
@@ -31,13 +31,14 @@ Imports:
     Rcpp (>= 0.11.2),
     scales (>= 0.4.0),
     plotly (>= 4.7.1),
-    magrittr (>= 1.5)
+    magrittr (>= 1.5),
+    rmarkdown(>= 1.6),
+    htmlwidgets (>= 1.0)
 Suggests:
     knitr,
-    rmarkdown,
     testthat (>= 0.9.0)
 SystemRequirements: C++11
 VignetteBuilder: knitr
 LinkingTo: Rcpp
 RoxygenNote: 6.0.1
-Date: 2017-08-09
+Date: 2018-05-18

DESCRIPTION

@@ -5,6 +5,8 @@ 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)
 export(dEploid)
 export(plotProportions)

NAMESPACE

@@ -25,7 +25,6 @@
 
 #include <iostream> // std::cout
 #include "mcmc.hpp"
-#include "panel.hpp"
 #include "dEploidIO.hpp"
 
 using namespace std;
@@ -46,10 +45,13 @@ int main( int argc, char *argv[] ){
             return EXIT_SUCCESS;
         }
 
-        if ( dEploidIO.doPainting() ){
+        if ( dEploidIO.doComputeLLK() ){
+            dEploidIO.computeLLKfromInitialHap();
+        } else if ( dEploidIO.doLsPainting() ){
             dEploidIO.chromPainting();
-        } else{
-
+        } else if ( dEploidIO.doIbdPainting() ){
+            dEploidIO.paintIBD();
+        }else{
             if (dEploidIO.useIBD()){ // ibd
                 McmcSample * ibdMcmcSample = new McmcSample();
                 MersenneTwister ibdRg(dEploidIO.randomSeed());
@@ -66,6 +68,8 @@ int main( int argc, char *argv[] ){
                                         false); // use IBD
             mcmcMachinery.runMcmcChain(true, // show progress
                                        false); // use IBD
+
+            dEploidIO.paintIBD();
             delete mcmcSample;
         }
         // Finishing, write log