preparing release 2.2.2

GATB · Jun 19, 2020 · fb93bcb · fb93bcb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,11 @@
 --------------------------------------------------------------------------------
 ## [Unreleased]
 
+--------------------------------------------------------------------------------
+## [2.2.2] - 2020-06-19
+
+* A bug fix: updating gatb-core version, notably this fixes a bug in the `fill` module: nodes at extremities of contigs of size exactly `k` were not marked correctly, potentially leading to duplicated contigs in the contig graph. This could prevent exploring some parts of the graph, and if graph exploration parameters where set too large (`-max-nodes` and `-max-length`), it could lead in some rare cases to extreme running times and/or memory consumptions. This should no longer happen now.
+
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 ## [2.2.1] - 2019-11-29
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -28,7 +28,7 @@ cmake_minimum_required(VERSION 3.1)
 # The default version number is the latest official build
 SET (gatb-tool_VERSION_MAJOR 2)
 SET (gatb-tool_VERSION_MINOR 2)
-SET (gatb-tool_VERSION_PATCH 1)
+SET (gatb-tool_VERSION_PATCH 2)
 
 # But, it is possible to define another release number during a local build
 IF (DEFINED MAJOR)

diff --git a/README.md b/README.md
@@ -62,17 +62,16 @@ In case the software does not run appropriately on your system, you should consi
     # the binary file is located in directory build/bin/
     ./build/bin/MindTheGap -help
 
-## Using docker or conda
+## Using conda or docker
 
-Pull the docker image of the latest release of MindTheGap:
+MindTheGap is also distributed as a [Bioconda package](https://anaconda.org/bioconda/mindthegap):
+
+    conda install -c bioconda mindthegap
 
-    docker pull clemaitr/mindthegap
+Or pull the docker image of MindTheGap (warning: need to be updated with latest releases):
 
-MindTheGap is also distributed as a [Bioconda package](https://anaconda.org/bioconda/mindthegap):
+    docker pull clemaitr/mindthegap
 
-``` 
-conda install -c bioconda mindthegap
-```
 
 
 
@@ -82,7 +81,7 @@ conda install -c bioconda mindthegap
 
 MindTheGap is a software that performs integrated detection and assembly of **genomic insertion variants** in NGS read datasets with respect to a reference genome. It is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. 
 
-Alternatively and since release 2.1.0, MindTheGap can also be used as a **genome assembly finishing tool**. It is integrated as an essential step in the **targeted assembly** tool [MinYS (MineYourSymbiont in metagenomics datasets)](https://github.com/cguyomar/MinYS).
+Alternatively and since release 2.1.0, MindTheGap can also be used as a **genome assembly finishing tool**. It is integrated as an essential step in the **targeted assembly** tool [MinYS (MineYourSymbiont in metagenomics datasets)](https://github.com/cguyomar/MinYS). It takes also part of a gap-filling pipeline dedicated to linked-read data (10X Genomics):  [MTG-link](https://github.com/anne-gcd/MTG-Link).
 
 **Insertion variant detection**
 

diff --git a/src/main.cpp b/src/main.cpp
@@ -26,7 +26,7 @@
 
 using namespace std;
 
-static const char* MTG_VERSION = "2.2.1";
+static const char* MTG_VERSION = "2.2.2";
 
 static const char* STR_FIND        = "find";
 static const char* STR_FILL = "fill";