Release v0.2.8

What's New

See individual changes below.

Features

• Script to recombine GVCFs based on a set of BED files detailing where the crossover points are.

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.8.tar - Unix/Linux/macOS
• seq_sim-v0.2.8.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.8.tar
# or
unzip seq_sim-v0.2.8.zip

# Run the application
./seq_sim-v0.2.8/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.7...v0.2.8

Release v0.2.7

What's New

See individual changes below.

Features

• Adds better defaults depending on prior steps for assembly lists
• Adds missing maf-to-gvcf step
• "QoL" updates to example pipeline YAML file

Bug Fixes

• Fixes issues with FASTA file extensions in the Python scripts

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.7.tar - Unix/Linux/macOS
• seq_sim-v0.2.7.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.7.tar
# or
unzip seq_sim-v0.2.7.zip

# Run the application
./seq_sim-v0.2.7/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.6...v0.2.7

Release v0.2.6

What's New

See individual changes below.

Features

• Replaced all ProcessRunner.runCommand("./gradlew", "run", ...) calls with direct Clikt command parsing via CommandName().parse(args). This eliminates the overhead of spawning new Gradle/JVM processes for each pipeline step.
• Added restoreOrchestratorLogging() to maintain proper log file separation after each step runs.
• All paths are now resolved to absolute, normalized paths for consistency. This prevents issues with relative path resolution when working directories change.
• Changed config section parsing from map?.let { ... } to if (configMap.containsKey(...)) pattern. This allows pipeline steps to run with defaults even when config section is empty/null (i.e., just specifying the key enables the step).
• Added missing parameter features in downsample_gvcf and covert_to_fasta steps.
• General "QoL" updates to example pipeline YAML file.

Bug Fixes

• Fixed biokotlin-tools gzip naming (biokotlin-tools automatically compresses output and adds .gz extension)
• Temporary directories are now always cleaned up if they exist, not just when files were actively used from them.
• Added cleanup of ALL existing file appenders when setting up a new log file
• Prevents log bleeding where messages from step $N + 1$ appear in step $N$'s log file
• Properly stops old appenders before removing them
• Corrected binary name issue where "biokotlin" was called instead of "biokotlin-tools"

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.6.tar - Unix/Linux/macOS
• seq_sim-v0.2.6.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.6.tar
# or
unzip seq_sim-v0.2.6.zip

# Run the application
./seq_sim-v0.2.6/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.5...v0.2.6

Release v0.2.5

What's New

See individual changes below.

Features

• None

Bug Fixes

• Fixed issue with calling gradle commands through CLI
• Fixed executable issue with MLImpute gradle commands
• Fixed Python module exceptions in steps needing to execute Python scripts

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.5.tar - Unix/Linux/macOS
• seq_sim-v0.2.5.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.5.tar
# or
unzip seq_sim-v0.2.5.zip

# Run the application
./seq_sim-v0.2.5/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.4...v0.2.5

Release v0.2.4

What's New

See individual changes below.

Features

• Changing the parameter names so they are more clear.

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.4.tar - Unix/Linux/macOS
• seq_sim-v0.2.4.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.4.tar
# or
unzip seq_sim-v0.2.4.zip

# Run the application
./seq_sim-v0.2.4/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.3...v0.2.4

Release v0.2.3

What's New

See individual changes below.

Features

• Command to take mutations from one gVCF and add to another.

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.3.tar - Unix/Linux/macOS
• seq_sim-v0.2.3.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.3.tar
# or
unzip seq_sim-v0.2.3.zip

# Run the application
./seq_sim-v0.2.3/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.1...v0.2.3

Release v0.2.1

What's New

See individual changes below.

Features

• None

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.1.tar - Unix/Linux/macOS
• seq_sim-v0.2.1.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.1.tar
# or
unzip seq_sim-v0.2.1.zip

# Run the application
./seq_sim-v0.2.1/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2...v0.2.1