From a9408419f77b8751dc2b25b8d744c82758bc18d6 Mon Sep 17 00:00:00 2001
From: Juliette Luiselli <juliette.luiselli@inria.fr>
Date: Tue, 22 Nov 2022 17:19:32 +0100
Subject: [PATCH] make sure no mutation occurs at the breaking point
---
src/libaevol/7/DnaMutator.cpp | 26 +++++++++++++++++++++++---
1 file changed, 23 insertions(+), 3 deletions(-)
diff --git a/src/libaevol/7/DnaMutator.cpp b/src/libaevol/7/DnaMutator.cpp
index d8ae17647..20917ac08 100644
--- a/src/libaevol/7/DnaMutator.cpp
+++ b/src/libaevol/7/DnaMutator.cpp
@@ -165,9 +165,14 @@ MutationEvent* DnaMutator::generate_next_mutation(int32_t length) {
if (pos_1 < pos_2) {
seqlen = pos_2 - pos_1;
} else {
- int32_t tmp1_len = length_ - pos_1;
- int32_t tmp2_len = pos_2;
- seqlen = tmp1_len + tmp2_len;
+ #ifdef __EUKARYOTE
+ Utils::exchange(pos_1, pos_2);
+ seqlen = pos_2 - pos_1;
+ #else
+ int32_t tmp1_len = length_ - pos_1;
+ int32_t tmp2_len = pos_2;
+ seqlen = tmp1_len + tmp2_len;
+ #endif
}
int32_t genome_size_after = length_ + seqlen;
@@ -206,8 +211,13 @@ MutationEvent* DnaMutator::generate_next_mutation(int32_t length) {
if (pos_1 < pos_2) {
genome_size_after = length_ - (pos_2 - pos_1);
} else {
+ #ifdef __EUKARYOTE
+ Utils::exchange(pos_1, pos_2);
+ genome_size_after = length_ - (pos_2 - pos_1);
+ #else
genome_size_after = length_ - (length_ - pos_1);
genome_size_after = genome_size_after - pos_2;
+ #endif
}
// printf("Remove %d %d : LB %d LA %d\n",pos_1,pos_2,length_,genome_size_after);
@@ -226,6 +236,9 @@ MutationEvent* DnaMutator::generate_next_mutation(int32_t length) {
}
else if (random_value < nb_large_dupl_ + nb_large_del_ + nb_large_trans_) {
+ #ifdef __EUKARYOTE
+ std::cout << "Warning : performing a translocation with a eukaryotic individual"<<std::endl;
+ #endif
nb_large_trans_--;
if (length_ == 1)
@@ -292,6 +305,7 @@ MutationEvent* DnaMutator::generate_next_mutation(int32_t length) {
// if (pos_1 == pos_2) return nullptr; // Invert everything <=> Invert nothing!
// Invert the segment that don't contain OriC
+ // Convenient for prokaryotes, absolutely necessary for eukaryotes
if (pos_1 > pos_2) Utils::exchange(pos_1, pos_2);
mevent = new MutationEvent();
@@ -374,6 +388,12 @@ MutationEvent* DnaMutator::generate_next_mutation(int32_t length) {
if (length_ - nb_pos_to_del < min_genome_length_)
return nullptr;
+
+ #ifdef __EUKARYOTE
+ if (pos + nb_pos_to_del > length_){
+ nb_pos_to_del = length_ - pos; // Doing the maximal possible deletion
+ }
+ #endif
length_ = length_ - nb_pos_to_del;
--
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