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Release 0.3.2 - #37

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qclayssen wants to merge 72 commits into

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release/0.3.2

Commits on Oct 2, 2025
- Add option for sash sigrap individual process input to cancer report (#11)
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  d7ca46b
- Hypermutation Handling in PCGR (#9)
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  f33c48c
- Feature/pcgr v2.2.1 (#10)
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  cb5ee4d
- fix merge duplication and imports
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  9d8e4d1
- bump pcgr version
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- bump gpgr version
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  c67b30a
Commits on Oct 16, 2025
- change print to logging
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  f9a7d3b
- add argument chunck size
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  b8ee4a0
Commits on Oct 17, 2025
- fix version software pcgr container
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  8223ef9
- add logging and filter fonction to read value and replace placeholder
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  f83c23a
- fix indentation
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  22b5c12
- read gz tsv from pcgr
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  529309c
Commits on Oct 20, 2025
- change PCGR_CLINVAR_CLASSIFICATION
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- Change pcgr header check
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Commits on Oct 24, 2025
- tyo
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  bf930e7
- typo
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  8ea1edc
- add missing variable pcgr_output_dir
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Commits on Nov 19, 2025
- Pcgr v2.2.5 (#22)
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Commits on Nov 24, 2025
- Uptade sage vcf header check (#24)
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  6a93f6b
- add missing HMF_HOTSPOT constant
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  ed3b11b
- Fix quotation
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- Fix test
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  9ddeac8
Commits on Dec 16, 2025
- remove PCGR html report from chunk (hypermutated) to reduce memory use
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  41b83bb
Commits on Dec 17, 2025
- change remove pcgr parallelisation of chunks, and fix pcgr internal parallelisation because OOM hypermutated samples
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  c42d725
- free disk worker
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  03bba1d
Commits on Dec 19, 2025
Commits on Dec 22, 2025
- Extract PCGR errors from log files
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  15db538
Commits on Jan 21, 2026
- Update bolt/workflows/other/cancer_report.py
  
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  Copilot
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  9bf22f5
- Update bolt/common/pcgr.py
  
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  599849d
Commits on Feb 19, 2026
- Apply suggestions from code review
  
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  09a3a24
- fix typo
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  dbd500f
- remove duplicate fonction
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  3d2d7b1
Commits on Feb 20, 2026
- fix typo
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  15f0247
- add check pcgr_hotspot_present value
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  8fa85ef
Commits on May 7, 2026
- add is_hypermutated flag to variant counts process JSON
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  31dabab
Commits on May 12, 2026
- update PCGR_TIERS_FILTERING
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  f3d557c
- Fix PCGR hypermutated filtering, add exhaustive tests
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  184e170
- add back source comment
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  5a28918
- DEV: install r-gpgr from input-sigrap-data branch for is_hypermutated testing
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  48488d6
Commits on May 13, 2026
- Add tests for split_vcf chunking and document PCGR 500k handling
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  b97d216
- Fix positional arg shift in run_somatic_chunk → run_somatic call
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  cc39768
Commits on May 14, 2026
- fix hypermutated tag
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  7f01001
- Add tests for is_hypermutated dragen count fix
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  97ad9f7
- Separate stdout/stderr streams in execute_command
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  b4ab71f
Commits on May 15, 2026
- Pin r-gpgr ==2.3.0 in Dockerfile.gpgr
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  1b366fa
- fix doc and missing file closure
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  f77deb4
- add test
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  1b6e28a
- change .with_suffix :
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  58987d1
- chore: untrack local-only files
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  5949539
- update CHANGELOG for 0.3.0 release
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  e0103ef
Commits on May 18, 2026
- bump version to 0.3.1 and update changelog
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  149db35
- ci: add smoke tests to catch image startup failures before push
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  358290a
Commits on May 19, 2026
Commits on May 24, 2026
- fix: bump r-gpgr to 2.3.1 in gpgr Docker image
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  d2c390f
Commits on Jun 2, 2026
- fix: skip PCGR when variant count exceeds MAX_SOMATIC_VARIANTS
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  d34bc05
- test: cover PCGR graceful skip on unresolvable variant count overflow
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Commits on Jun 3, 2026
Commits on Jun 9, 2026
- change: drop --estimate_signatures from PCGR somatic invocation (#31)
  
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  Copilot
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Commits on Jul 3, 2026
- docs: update CHANGELOG for fixes landed since v0.3.1 tag
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- Fix/52 pcgr skip high variant count (#32)
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- Merge remote-tracking branch 'origin/release/0.3.0' into release/0.3.0
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  05a9abc
- fix: pin free-disk-space action, disable_estimates in chunked PCGR, logger.info cleanup
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- Merge branch 'fix/52-pcgr-skip-high-variant-count'
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- Bump version: 0.3.1 → 0.3.2
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- style: remove obvious comments and docstrings from util.py
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  91c5d3c

Commits

Commits on Oct 2, 2025

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