Release/0.3.0

[qclayssen]

Add

• Hypermutation Handling
• option for sigrap individual process

Upgrade

• pcgrr v1.4.1 -> pcgr v2.2.1

[Copilot]

Pull Request Overview

This PR upgrades PCGR from v1.4.1 to v2.2.1 and adds handling for hypermutated samples. The upgrade requires updating field names and annotations to match the new PCGR version's output format, while new functionality filters variants in hypermutated samples to stay within PCGR's variant count limits.

Key changes:

• Updated PCGR/CPSR field names to match v2.2.1 output (e.g., PCGR_TIER → PCGR_ACTIONABILITY_TIER)
• Added hypermutation handling with variant filtering logic for samples exceeding 450,000 variants
• Implemented chunked PCGR processing for large variant sets with parallel execution

Reviewed Changes

Copilot reviewed 19 out of 20 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
pyproject.toml	Version bump to 0.2.17
docker/Dockerfile.pcgr	Updated PCGR conda environment from v1.4.1 to v2.2.1
docker/Dockerfile.gpgr	Updated r-gpgr from 2.1.3 to 2.2.11
conda/env/bolt_env.yml	Added ncurses dependency
bolt/workflows/sv_somatic/annotate.py	Added logging infrastructure
bolt/workflows/smlv_somatic/rescue.py	Added logging infrastructure
bolt/workflows/smlv_somatic/report.py	Added hypermutation variant filtering and updated PCGR integration
bolt/workflows/smlv_somatic/filter.py	Updated field names for PCGR v2.2.1 and added helper function to handle missing values
bolt/workflows/smlv_somatic/annotate.py	Refactored PCGR processing to support chunking and updated field names
bolt/workflows/smlv_germline/report.py	Added logging and vep_dir parameter
bolt/workflows/other/cancer_report.py	Made dragen_hrd_fp optional and added new signature analysis parameters
bolt/util.py	Enhanced command execution with logging, added VCF splitting/merging utilities
bolt/logging_config.py	New logging configuration module
bolt/common/pcgr.py	Major refactor for PCGR v2.2.1 compatibility, chunked processing, and updated field mappings
bolt/common/constants.py	Updated field names and added hypermutation filtering constants
tests/test_smlv_somatic_filter.py	Updated test data to match new PCGR field names
README.md	Updated version references to 0.2.17
CHANGELOG.md	Added changelog entries for recent PRs
.bumpversion.cfg	Updated version to 0.2.17

Comments suppressed due to low confidence (1)

bolt/common/pcgr.py:1

• Missing spaces around the == operator. Should be if value == '' or value == '.':

import collections

---

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[Copilot]

Missing space before the = operator. Should be data['difficult'] = False

Suggested change

	data['difficult']= False
	data['difficult'] = False

[Copilot]

[nitpick] Inconsistent quote usage in f-string. Line 118 uses double quotes inside curly braces while line 106 uses single quotes. For consistency, use single quotes: {kwargs['tumor_name']}

[Copilot]

Missing space after the hyphen. Should be - [9] for consistency with other entries.

Suggested change

	-[9](https://github.com/umccr/bolt/pull/9) Add hypermutation sample handling
	- [9](https://github.com/umccr/bolt/pull/9) Add hypermutation sample handling