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Release v0.3.0

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@github-actions github-actions released this 25 May 15:03
· 54 commits to main since this release
v0.3.0
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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

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