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Release v0.5.0

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@github-actions github-actions released this 08 Jul 13:53
v0.5.0
5d89d81
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What's New

See individual changes below.

Features

  • Add OrchestrateV2E2ETest covering entire "end-to-end" pipeline
  • Add --disable-asm-coordinates flag to build-spline-knots (CLI, YAML config, and OrchestrateV2 wiring) for gVCFs that lack valid ASM_Start/ASM_End coordinates

Bug Fixes

  • Fix bcftools sort failures on recombined gVCFs missing ##contig header declarations
  • Fix PHG gamete resolution failures when recombined sample names contained underscores

Breaking Changes

  • Change recombined gVCF output files from {target}_recombined.gvcf to {target}-recombined.gvcf

Installation

Download the appropriate archive for your system:

  • seq_sim-v0.5.0.tar - Unix/Linux/macOS
  • seq_sim-v0.5.0.zip - Windows

Quick Start

# Extract the archive
tar -xf seq_sim-v0.5.0.tar
# or
unzip seq_sim-v0.5.0.zip

# Run the application
./seq_sim-v0.5.0/bin/seq_sim --help

Requirements

  • Java 21 or higher

Full Changelog

Full Changelog: v0.4.4...v0.5.0

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