preparing v2.3.0

CHANGELOG.md

@@ -3,6 +3,16 @@
 --------------------------------------------------------------------------------
 ## [Unreleased]
 
+--------------------------------------------------------------------------------
+## [2.3.0] - 2022-04-20
+
+Improving the `Find` (insertion breakpoint finder) module:
+
+* very small insertions (1 or 2 bp) are now directly assembled in the `Find` module and are output in the `.othervariants.vcf` file. This may increase the running time of the `Find` module but the overall running time of MindTheGap (Find+Fill) is drastically reduced. Indeed, these numerous small insertions are no longer output in the breakpoint file, nor given as input for the `Fill` assembly module which performs a deeper traversal of the de Bruijn graph (designed for longer insertions). 
+* a novel filter is implemented to reduce the amount of False Positive insertion sites. It is based on the number of branching kmers in a 100-bp window before a heterozygous site. It can be tuned with the novel option `-branching-filter`. It is now activated by default, so this may modify the amount of heterozygous sites detected with respect to previous versions. 
+
+With this new version, the running time of MindTheGap as an insertion variant caller is reduced for real large datasets, such as human genome re-sequencing data. 
+
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 ## [2.2.3] - 2021-06-11
 

CMakeLists.txt

@@ -27,8 +27,8 @@ 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 3)
+SET (gatb-tool_VERSION_MINOR 3)
+SET (gatb-tool_VERSION_PATCH 0)
 
 # But, it is possible to define another release number during a local build
 IF (DEFINED MAJOR)

doc/MindTheGap_insertion_caller.md

@@ -52,7 +52,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module
 
     In addition to the read or graph files, the `fill` module has one other mandatory option, `-bkpt`:
 
-    * `-bkpt`: the breakpoint file path. This is one of the output of the `find` module and contains for each detected insertion site its left and right kmers from and to which the local assembly will be performed (see section E for details about the format).
+    * `-bkpt`: the breakpoint file path. This is one of the output of the `find` module and contains for each detected insertion site its left and right kmers from and to which the local assembly will be performed (see section [Output formats](#output-formats) for details about the format).
 
 	The fill module has several optional options:
 
@@ -83,6 +83,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module
 
 
 ## Details on output formats
+<a name="output-formats"></a>
 
 1. Breakpoint format
 

src/main.cpp

@@ -26,7 +26,7 @@
 
 using namespace std;
 
-static const char* MTG_VERSION = "2.2.3";
+static const char* MTG_VERSION = "2.3.0";
 
 static const char* STR_FIND        = "find";
 static const char* STR_FILL = "fill";