From d1f889b8c0d11cfde5e45dcb8955548c72265271 Mon Sep 17 00:00:00 2001
From: cristianetaniguti <chaytaniguti@gmail.com>
Date: Thu, 14 Dec 2023 21:46:43 -0600
Subject: [PATCH] add exception

---
 R/est_map_hmm.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/est_map_hmm.R b/R/est_map_hmm.R
index ef385d02..48bbc4a4 100755
--- a/R/est_map_hmm.R
+++ b/R/est_map_hmm.R
@@ -621,6 +621,11 @@ est_rf_hmm_sequential <- function(input.seq,
     submap.expansion <- submap.length.new - submap.length.old
     last.mrk.expansion <- last.dist.new - last.dist.old
     
+    if(length(M[,2]) == 0) {
+      if(verbose) cat(crayon::italic$yellow(paste0(ct ,": not included (~map extension~)\n", sep = "")))
+      ct <- ct + 1
+      next()
+    }
     
     cur.map.temp$maps <- cur.map.temp$maps[M[,2]]
     LOD <- get_LOD(cur.map.temp, sorted = FALSE)