From fe85c308434a4ad1ae7977dad67e966abc2bf93e Mon Sep 17 00:00:00 2001 From: Claire Lemaitre Date: Wed, 20 Apr 2022 16:18:46 +0200 Subject: [PATCH] preparing v2.3.0 --- CHANGELOG.md | 10 ++++++++++ CMakeLists.txt | 4 ++-- doc/MindTheGap_insertion_caller.md | 3 ++- src/main.cpp | 2 +- 4 files changed, 15 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc83b28..0864515 100644 --- a/CHANGELOG.md +++ b/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. + -------------------------------------------------------------------------------- ## [2.2.3] - 2021-06-11 diff --git a/CMakeLists.txt b/CMakeLists.txt index 3a89ffa..2bd895d 100644 --- a/CMakeLists.txt +++ b/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) diff --git a/doc/MindTheGap_insertion_caller.md b/doc/MindTheGap_insertion_caller.md index 8434b47..543f074 100644 --- a/doc/MindTheGap_insertion_caller.md +++ b/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 + 1. Breakpoint format diff --git a/src/main.cpp b/src/main.cpp index e2640d2..02ed17d 100644 --- a/src/main.cpp +++ b/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";