From 2a902eec247895ceeb810f7936857929431e2dc5 Mon Sep 17 00:00:00 2001
From: iminkin <ivminkin@gmail.com>
Date: Thu, 29 Sep 2022 00:16:45 -0400
Subject: [PATCH] Added necessary changes to keep up with TBB

---
 CMakeLists.txt                      | 2 +-
 NEWS.md                             | 6 ++++++
 README.md                           | 4 ++--
 SibeliaZ-LCB/CMakeLists.txt         | 1 -
 SibeliaZ-LCB/blocksfinder.cpp       | 2 +-
 SibeliaZ-LCB/sibeliaz               | 2 +-
 TwoPaCo                             | 2 +-
 examples/sibeliaz_out/alignment.maf | 2 +-
 8 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 789e9b3..b94a6f4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.0)
-project(SibeliaZ VERSION 1.2.4)
+project(SibeliaZ VERSION 1.2.5)
 set(CMAKE_POLICY_DEFAULT_CMP0048 NEW)
 
 include(ExternalProject)
diff --git a/NEWS.md b/NEWS.md
index 65732bb..54147df 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+SibeliaZ 1.2.5
+==============
+* Necessary updates to keep up with changes in TBB
+* Updated the readme: added more detailed clarification for the
+parameter -a (vertex frequency threshold)
+
 SibeliaZ 1.2.4
 ==============
 * Made GFF output compliant with the [GFF3 specification](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
diff --git a/README.md b/README.md
index 488e6b7..1bc8bec 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,9 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sibeliaz/README.html)
 
-SibeliaZ 1.2.4
+SibeliaZ 1.2.5
 ===============
 
-Release date: 6th September 2021
+Release date: 29th September 2022
 ================================
 
 Authors
diff --git a/SibeliaZ-LCB/CMakeLists.txt b/SibeliaZ-LCB/CMakeLists.txt
index d4402d4..09b9880 100644
--- a/SibeliaZ-LCB/CMakeLists.txt
+++ b/SibeliaZ-LCB/CMakeLists.txt
@@ -1,5 +1,4 @@
 project(SibeliaZ-LCB CXX)
-cmake_minimum_required(VERSION 2.8)
 set(CMAKE_BUILD_TYPE RELEASE)
 set(CMAKE_PROJECT_NAME sibeliaz)
 
diff --git a/SibeliaZ-LCB/blocksfinder.cpp b/SibeliaZ-LCB/blocksfinder.cpp
index 1c3dcf6..2f59953 100644
--- a/SibeliaZ-LCB/blocksfinder.cpp
+++ b/SibeliaZ-LCB/blocksfinder.cpp
@@ -27,7 +27,7 @@ namespace Sibelia
 	}
 
 	JunctionStorage * JunctionStorage::this_;
-	extern const std::string VERSION = "1.2.4";
+	extern const std::string VERSION = "1.2.5";
 
 	bool compareById(const BlockInstance & a, const BlockInstance & b)
 	{
diff --git a/SibeliaZ-LCB/sibeliaz b/SibeliaZ-LCB/sibeliaz
index a6f540f..1d6338b 100755
--- a/SibeliaZ-LCB/sibeliaz
+++ b/SibeliaZ-LCB/sibeliaz
@@ -120,7 +120,7 @@ global_alignment()
 {
 	echo "Performing global alignment.."
         echo "##maf version=1" > "$outfile"
-	echo "# sibeliaz v1.2.4 " >> "$outfile"
+	echo "# sibeliaz v1.2.5 " >> "$outfile"
 	echo "# cmd=$1" >> "$outfile"
 
 	memory_min=`free -k -w | head -2 | tail -1 | awk '{print $2}'`
diff --git a/TwoPaCo b/TwoPaCo
index b8e9f73..292d8ea 160000
--- a/TwoPaCo
+++ b/TwoPaCo
@@ -1 +1 @@
-Subproject commit b8e9f73b5687ccbd0bcc8b22c4e12d60fdce3fb6
+Subproject commit 292d8eaf4c9c736d555aadbb3ebc22dcdcdc4cb0
diff --git a/examples/sibeliaz_out/alignment.maf b/examples/sibeliaz_out/alignment.maf
index eb4e441..1141e90 100644
--- a/examples/sibeliaz_out/alignment.maf
+++ b/examples/sibeliaz_out/alignment.maf
@@ -1,5 +1,5 @@
 ##maf version=1
-# sibeliaz v1.2.4 
+# sibeliaz v1.2.5 
 # cmd=genome1.fa genome2.fa
 
 a