Improve hill climbing for constrained case

Minor changes to resolve issues in compiling on Mac

README.md

@@ -95,6 +95,11 @@ You may use the provided bash scripts to run the programs.
 > bash run-svtreemcmc.sh
 ```
 
+The most recent Mac switched to zsh. In that case, replace bash with zsh in the commands above.
+However, there may be issues running the commands on Mac with zsh.
+
+
+
 
 # Simulation with sveta
 SVETA simulates structural variations that alter copy numbers along a coalescence tree of multiple samples.
@@ -204,8 +209,8 @@ The last three modes can be used to validate the computation of likelihood.
 
 There are 3 tree searching method:
 * exhaustive search (feasible for trees with fewer than 7 samples)
-* hill climbing (only works for unconstrained case for now)
-* genetic algorithm (may be slow, need improvement, not recommend to use)
+* hill climbing (applicable for trees with at least 5 samples)
+* genetic algorithm (may be slow, need improvement, deprecated)
 
 Please see run-svtreeml.sh to learn how to set different parameters
 

ana/plot-cns.R

@@ -10,7 +10,7 @@ if(!require(optparse)){
     library(optparse)
 }
 
-# load("../../lpWGS phylogenies/bin_locations_4401.Rdata")
+
 #load("./bin_locations_4401.Rdata")
 
 # args = commandArgs(trailingOnly=TRUE)
@@ -40,7 +40,7 @@ out.file <- opt$out_file
 pattern <- opt$pattern
 
 plot_type <- "all"
-if(in.file!=""){
+if(in.file != ""){
   plot_type <- "single"
 }
 
@@ -114,7 +114,6 @@ if(0){  # test
 }
 
 if (plot_type == "all"){
-  #dir <- "../sim-data/"
   dir <- data.dir
   cat(paste0("Plotting all related files in directory ", dir, "\n"))
   if(pattern == ""){