Release v0.4.4

What's New

See individual changes below.

Features

• None

Bug Fixes

• Fixing the resizing regions issues from recombine gvcfs

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.4.4.tar - Unix/Linux/macOS
• seq_sim-v0.4.4.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.4.4.tar
# or
unzip seq_sim-v0.4.4.zip

# Run the application
./seq_sim-v0.4.4/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.4.3...v0.4.4

Release v0.4.3

What's New

See individual changes below.

Features

• Add v2 orchestrate steps:
• Add necessary FASTQ input to YAML
• Updates to example docs
• Refactor orchestrator logging banners into shared OrchestrateShared.logBanner() (used by OrchestrateV1 and OrchestrateV2)

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.4.3.tar - Unix/Linux/macOS
• seq_sim-v0.4.3.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.4.3.tar
# or
unzip seq_sim-v0.4.3.zip

# Run the application
./seq_sim-v0.4.3/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.4.2...v0.4.3

Release v0.4.2

What's New

See individual changes below.

Features

• Adds pick-base-crossovers step
• Integrate recombine-gvcfs into the v2 pipeline
• Adds sort-gvcfs which is a thin wrapper to bcftools sort
• Update example v2 YAML config for additional steps

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.4.2.tar - Unix/Linux/macOS
• seq_sim-v0.4.2.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.4.2.tar
# or
unzip seq_sim-v0.4.2.zip

# Run the application
./seq_sim-v0.4.2/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.4.1...v0.4.2

Release v0.4.1

What's New

See individual changes below.

Features

• Adds split-gvcfs command for splitting into "base" and "donor" sub-directories (mainly needed for automation purposes)
• Extends mutate-assemblies command with a "batch-mode". Adds the parameters: --keyfile, --base-dir, and --mutation-donor-dir.
• Adds highlighted steps into OrchestrateV2 automation chain
• Adds initial draft for example v2 YAML
• Adds unit tests for split-gvcfs and mutate-assemblies batch mode

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.4.1.tar - Unix/Linux/macOS
• seq_sim-v0.4.1.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.4.1.tar
# or
unzip seq_sim-v0.4.1.zip

# Run the application
./seq_sim-v0.4.1/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.4.0...v0.4.1

Release v0.4.0

What's New

See individual changes below.

Features

• Add a top-level version field ("v1"/"v2") to the orchestrate YAML config. If missing, this will default to "v1".
• Adds initial v2 pipeline (currently only generates initial gVCFs from AnchorWave)
• Refactor Orchestrate.run() to be a thin wrapper for version dispatch.
• Refactor orchestration into "v1", "v2", and "helper" objects.

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.4.0.tar - Unix/Linux/macOS
• seq_sim-v0.4.0.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.4.0.tar
# or
unzip seq_sim-v0.4.0.zip

# Run the application
./seq_sim-v0.4.0/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.3.0...v0.4.0

Release v0.3.0

What's New

See individual changes below.

Features

• Add commands/align/ shared module (PhgAlignParams, PhgAlignRunner, PhgAlignSharedOptions) and rewrite align-assemblies and align-mutated-assemblies as thin wrappers around PHGv2's align-assemblies (drives AnchorWave + minimap2 internally) while preserving the existing --ref-gff / --ref-fasta / --query-fasta / maf_file_paths.txt contract.
• Add new PHGv2 alignment knobs to both align steps and the YAML config: --in-parallel, --ref-max-align-cov, --query-max-align-cov, --conda-env-prefix, --just-ref-prep.
• Add ropebwt_mem, build_spline_knots, and convert_ropebwt2ps4g sections to orchestrate with output auto-chaining and config dataclasses.
• Add mutated-maf-to-gvcf as a documented orchestrate-only step 11.
• Add a separate Gradle e2eTest task and applyHeavyTestConfig() helper that forks one JVM per heavy test class and restricts class-file scanning so a single fork failure doesn't blow up the whole task.
• Add various Docker improvements for better integration with pixi environments and larger local test memory usage.
• Add IntegrationGuard test helper and ~17 new unit test files covering every pipeline command (AlignAssemblies, AlignMutatedAssemblies, ConvertCoordinates, ConvertRopebwt2Ps4g, ConvertToFasta, CreateChainFiles, DownsampleGvcf, FormatRecombinedFastas, GenerateRecombinedSequences, MafToGvcf, PickCrossovers, RopeBwtChrIndex, RopeBwtMem, PhgAlignRunner) plus a substantially expanded OrchestrateE2ETest.
• Add PHGv2 binary existence check to orchestrate's environment validation so missing PHG triggers an automatic setup-environment retry.

Bug Fixes

• Fix setup-environment failing to find the extracted MLImpute directory after the upstream repo was renamed to grits (archive extracts as grits-main/).
• Fix ropebwt-mem auto-calculating the wrong -l value: the keyfile written by rope-bwt-chr-index/orchestrate has no header row, so the previous lines.size - 1 count was off by one.
• Fix pixi and PHGv2 install permission failures with Docker.

Breaking Changes

• Minor renumbering of pipeline steps (added to docs).
• align-* steps now use PHGv2 instead of AnchorWave directly.

Installation

Download the appropriate archive for your system:

• seq_sim-v0.3.0.tar - Unix/Linux/macOS
• seq_sim-v0.3.0.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.3.0.tar
# or
unzip seq_sim-v0.3.0.zip

# Run the application
./seq_sim-v0.3.0/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.9...v0.3.0

Release v0.2.9

What's New

See individual changes below.

Features

• Add Docker dev stack to bake AnchorWave, PHGv2, and related tooling for Linux.
• Add scripts for building Docker image and testing (unit and integration)
• Update build.gradle.kts for different testing approaches
• Add new documentation to reflect clikt commands
• Add some initial tests to be fleshed out in a future update
• Add smallseq test data
• Add testing component to PR checks

Bug Fixes

• None

Breaking Changes

• None

Installation

Download the appropriate archive for your system:

• seq_sim-v0.2.9.tar - Unix/Linux/macOS
• seq_sim-v0.2.9.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.2.9.tar
# or
unzip seq_sim-v0.2.9.zip

# Run the application
./seq_sim-v0.2.9/bin/seq_sim --help

Requirements

• Java 21 or higher

Full Changelog

Full Changelog: v0.2.8...v0.2.9

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