From 2215f29d6df172868ad9f2a7fd69bf51f40f3a92 Mon Sep 17 00:00:00 2001
From: AudreyAAMartin <122282773+AudreyAAMartin@users.noreply.github.com>
Date: Thu, 9 Feb 2023 21:02:40 +0000
Subject: [PATCH] Fix to issue 110 (sortPed)

---
 R/crossing.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/crossing.R b/R/crossing.R
index dbbcb5a3..2be57efb 100644
--- a/R/crossing.R
+++ b/R/crossing.R
@@ -663,24 +663,24 @@ sortPed = function(id, mother, father, maxCycle=100){
     for(i in which(unsorted)){
       if(is.na(output$mother[i])&is.na(output$father[i])){
         # Is a founder
-        output$gen[i] = gen
+        output$gen[i] = 1
         unsorted[i] = FALSE
       }else if(is.na(output$mother[i])){
         # Mother is a founder
         if(!unsorted[output$father[i]]){
-          output$gen[i] = gen
+          output$gen[i] = output$gen[output$father[i]] + 1
           unsorted[i] = FALSE
         }
       }else if(is.na(output$father[i])){
         # Father is a founder
         if(!unsorted[output$mother[i]]){
-          output$gen[i] = gen
+          output$gen[i] = output$gen[output$mother[i]] + 1
           unsorted[i] = FALSE
         }
       }else{
         # Both parents are in the pedigree
         if(!unsorted[output$mother[i]] & !unsorted[output$father[i]]){
-          output$gen[i] = gen
+          output$gen[i] = pmax(output$gen[output$mother[i]], output$gen[output$father[i]]) + 1
           unsorted[i] = FALSE
         }
       }