From cb4cf2223925527306ed925b6bffeca549691f7c Mon Sep 17 00:00:00 2001
From: xiangpin <xshuangbin@163.com>
Date: Mon, 8 Mar 2021 17:46:20 +0800
Subject: [PATCH 1/3] update read.beast

---
 R/beast.R | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/R/beast.R b/R/beast.R
index d0b9f9e..68db8a2 100644
--- a/R/beast.R
+++ b/R/beast.R
@@ -175,8 +175,16 @@ read.stats_beast_internal <- function(beast, tree) {
         ## BEAST output
         stats <- strsplit(tree, ":") %>% unlist
     }
-
-    names(stats) <- node
+    
+    # check whether the stats info is after edge length or not.
+    if (!all(grepl("]$", stats) || grepl("];$", stats))){
+        # t1:0.04[&mutation="test1"]
+        stats <- sub("].*", "", stats)
+        names(stats) <- c(rep(node[1],2),node[-c(1,length(node))])
+    }else{
+        # t1[&mutation="test1"]:0.04
+        names(stats) <- node
+    }
 
     stats <- stats[grep("\\[", stats)]
     stats <- sub("[^\\[]*\\[", "", stats)
@@ -184,12 +192,17 @@ read.stats_beast_internal <- function(beast, tree) {
     stats <- sub("^&", "", stats)
     stats <- sub("];*$", "", stats)
     stats <- gsub("\"", "", stats)
-
+    
     stats2 <- lapply(seq_along(stats), function(i) {
         x <- stats[[i]]
         y <- unlist(strsplit(x, ","))
-        sidx <- grep("=\\{", y)
-        eidx <- grep("\\}$", y)
+        # the stats information has not always {}
+        #sidx <- grep("=\\{", y)
+        #eidx <- grep("\\}$", y)
+        # [&mutation="test1,test2",rate=80,90]
+        sidx <- grep("=", y)
+        eidx <- sidx - 1
+        eidx <- c(eidx[-1], length(y))
 
         flag <- FALSE
         if (length(sidx) > 0) {

From 2938b4d1f53d790822cdc72673fea28d9f73d6bd Mon Sep 17 00:00:00 2001
From: xiangpin <xshuangbin@163.com>
Date: Tue, 9 Mar 2021 15:51:16 +0800
Subject: [PATCH 2/3] better parse single value to single key in stats infor of
 beast

---
 R/beast.R | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/R/beast.R b/R/beast.R
index 68db8a2..04d71cb 100644
--- a/R/beast.R
+++ b/R/beast.R
@@ -192,18 +192,21 @@ read.stats_beast_internal <- function(beast, tree) {
     stats <- sub("^&", "", stats)
     stats <- sub("];*$", "", stats)
     stats <- gsub("\"", "", stats)
-    
+
     stats2 <- lapply(seq_along(stats), function(i) {
         x <- stats[[i]]
         y <- unlist(strsplit(x, ","))
-        # the stats information has not always {}
+        # the stats information does not has always {}
         #sidx <- grep("=\\{", y)
         #eidx <- grep("\\}$", y)
         # [&mutation="test1,test2",rate=80,90]
-        sidx <- grep("=", y)
-        eidx <- sidx - 1
-        eidx <- c(eidx[-1], length(y))
-
+        sidx1 <- grep("=", y)
+        eidx1 <- sidx1 - 1
+        eidx1 <- c(eidx1[-1], length(y))
+        # for better parsing [&mutation="test",name="A"] single value to key.
+        sidx <- sidx1[!(sidx1==eidx1)]
+        eidx <- eidx1[!(sidx1==eidx1)]
+        
         flag <- FALSE
         if (length(sidx) > 0) {
             flag <- TRUE

From bf379f92b383c3420b0bdda72cfa7305db80aa40 Mon Sep 17 00:00:00 2001
From: xiangpin <xshuangbin@163.com>
Date: Wed, 10 Mar 2021 10:09:34 +0800
Subject: [PATCH 3/3] remove elements before = in values of annotation

---
 R/beast.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/beast.R b/R/beast.R
index 04d71cb..be532e5 100644
--- a/R/beast.R
+++ b/R/beast.R
@@ -212,7 +212,9 @@ read.stats_beast_internal <- function(beast, tree) {
             flag <- TRUE
             SETS <- lapply(seq_along(sidx), function(k) {
                 p <- y[sidx[k]:eidx[k]]
-                gsub(".*=\\{", "", p) %>% gsub("\\}$", "", .)
+                gsub(".*=\\{", "", p) %>% 
+                    gsub("\\}$", "", .) %>%
+                    gsub(".*=", "", .)
             })
             names(SETS) <- gsub("=.*", "", y[sidx])