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Bump version to 0.10.0 and update the README.md #264

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Oct 15, 2024
Merged

Bump version to 0.10.0 and update the README.md #264

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cd61f7c
Bump version to 0.10.0 and update the README.md
tcezard Oct 15, 2024
5d9a464
fix typo
tcezard Oct 15, 2024
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4 changes: 2 additions & 2 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ cmake_minimum_required (VERSION 2.8)
project (vcf-validator CXX C)

set (vcf-validator_VERSION_MAJOR 0)
set (vcf-validator_VERSION_MINOR 9)
set (vcf-validator_VERSION_PATCH 7)
set (vcf-validator_VERSION_MINOR 10)
set (vcf-validator_VERSION_PATCH 0)

configure_file (
"${PROJECT_SOURCE_DIR}/inc/cmake_config.hpp.in"
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21 changes: 4 additions & 17 deletions README.md
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Expand Up @@ -13,11 +13,11 @@ These tools have been implemented using C++11.

### From Binaries

The vcf-validator is built with all the dependencies included. It can be downloaded directly from the [latest release](https://github.com/EBIvariation/vcf-validator/releases) for the most stable experience using vcf-validator. Along with the release notes, you will find the executables `vcf_validator` and `vcf_assembly_checker` for Linux, macOS and Windows. For Windows, please also download the libraries in the [lib/windows_specific/](https://github.com/EBIvariation/vcf-validator/tree/master/lib/windows_specific/) folder.
The vcf-validator is built with all the dependencies included. It can be downloaded directly from the [latest release](https://github.com/EBIvariation/vcf-validator/releases) for the most stable experience using vcf-validator. Along with the release notes, you will find the executables `vcf_validator` and `vcf_assembly_checker` for Linux, macOS and Windows.

### From conda

Starting from [v0.9.6](https://github.com/EBIvariation/vcf-validator/releases/tag/v0.9.6), you can install vcf-validator via conda using
Starting from [v0.9.6](https://github.com/EBIvariation/vcf-validator/releases/tag/v0.9.6), you can install vcf-validator on Linux and Mac via conda using

```
conda install -c bioconda vcf-validator
Expand Down Expand Up @@ -54,10 +54,6 @@ Each report is written into its own file and it is named after the input file, f

A flag for validating evidence can be passed with `--require-evidence`. This will validate whether the VCF includes either Genotypes or Allele Frequencies. This flag will be **false** by default.

### Debugulator

Removed debugulator support and ODB dependency.

### Assembly Checker

vcf-assembly-checker assesses the correctness of a VCF file with respect to a FASTA file (that should contain the reference sequence). The assembly checker reads the CHR, POS and REF columns from the VCF, and for each line, looks into the FASTA file to see if the REF allele matches that region. A VCF file is considered valid if all the variants match the sequence in the FASTA file.
Expand Down Expand Up @@ -139,7 +135,7 @@ If you are using Ubuntu 16, you can prepare all dependencies and compile the Val
```
sudo apt-get install cmake wget build-essential
./install_dependencies.sh linux
mkdir build && cd build && cmake -G "Unix Makefiles" ..
mkdir build && cd build && cmake -G "Unix Makefiles" -DSTATIC_BUILD=1 ..
make
```

Expand All @@ -148,7 +144,7 @@ The VCF Validation Suite binaries will be created in the `build/bin` subfolder.
##### CMake and automatic installation
The automatic install **requires** CMake and wget to be installed before running the script (as zlib require them to be installed). Also, the script will compile some dependencies so a compilation environment is needed. If you are using Ubuntu, you can install all that with the command `sudo apt-get install cmake wget build-essential`. After installing that, use the command `./install_dependencies.sh linux`.

A subfolder named `linux_dependencies` will be created, with all the required libraries copied into it.
A subfolder named `dependencies` will be created, with all the required libraries copied into it.

##### Boost

Expand All @@ -157,10 +153,6 @@ A subfolder named `linux_dependencies` will be created, with all the required li
The dependencies are the Boost library core, and its submodules: Boost.filesystem, Boost.iostreams, Boost.program_options, Boost.regex, Boost.log and Boost.system.
If you are using Ubuntu, you can install them with the command `sudo apt-get install libboost-dev libboost-filesystem-dev libboost-iostreams-dev libboost-program-options-dev libboost-regex-dev libboost-log-dev`.

##### ODB

ODB dependency is removed, ODB and debugulator are no longer in build.

#### Compile

In order to create the build scripts, please run `cmake` with your preferred generator. For instance, `mkdir build && cd build && cmake -G "Unix Makefiles" ..` will create Makefiles, and to build the binaries, you will need to run `make`.
Expand All @@ -186,7 +178,6 @@ Boost | \>=1.65 | manual
You can prepare all dependencies and compile the Validation Suite with these commands:
```
brew install cmake boost sqlite3
./install_dependencies.sh osx
mkdir build && cd build && cmake -G "Unix Makefiles" ..
make
```
Expand Down Expand Up @@ -226,10 +217,6 @@ bootstrap
* Add boost_1_xx_x/stage/lib folder to the environment variable `LIB`
* Add boost_1_xx_x folder to the environment variable `INCLUDE`

##### ODB

ODB dependency is removed, ODB and debugulator are no longer in build.

#### Compile

In order to create the build scripts and compile vcf-validator, please run the following commands from the project root folder:
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