OA-only mode: handle oncoanalyser-only inputs (no DRAGEN) - #34
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qclayssen wants to merge 67 commits into
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OA-only mode: handle oncoanalyser-only inputs (no DRAGEN)#34qclayssen wants to merge 67 commits into
qclayssen wants to merge 67 commits into
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…11) * add params input for sigrap tools
* update "HIGH_INF_POS" to "HIGH_I_I_POS" in VCF header for latest pcgr version * update constant for pcgr 2.2.5
* change sage vcf header to match 2024 version * move check function * add check in rescue for sage vcf * change for consistencency with pcgr
…arallelisation because OOM hypermutated samples
…'t use more core and so more memory
…e_command. Fixes #26 - Commands now fail immediately instead of continuing silently
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Uses select() to multiplex both pipes in one thread, preventing pipe buffer deadlock and routing stderr to WARNING level.
Includes hypermutated flag fix (reads is_hypermutated from bolt JSON) and SNVs display cleanup.
Path.with_suffix() only replaces the last suffix everything after the final dot. The caller passes a path ending in .pass
….2.5 tabix check)
- smlv_somatic report: make --vcf_dragen_fp optional; skip dragen/bolt variant count comparison when absent; filt_* fields set to None in MultiQC YAML output - transfer_annotations_germline: handle CPSR writing no output files when zero variants pass filtering; treat absent TSV/VCF as empty annotation data and pass variants through unchanged
SAGE sets GT=./. for all variants; CPSR drops all records with missing genotype at report generation. Convert ./. to 0/1 via bcftools +setGT so CPSR produces meaningful germline predisposition output in OA-only mode.
PCGR can emit multiple rows for the same variant when it maps to multiple transcripts. Replace assert with tier-aware deduplication: keep the most actionable entry (lowest tier number), warn on duplicates.
Add PCGR_TIER_NORMALISE dict to constants.py; derive _TIER_ORDER from PCGR_TIERS_FILTERING. Removes inline tier string literals from pcgr.py.
PCGR can emit duplicate variant entries in its output VCF. The assert raised on the second occurrence; skip duplicates with a warning instead.
SQ is a DRAGEN FORMAT field; cyvcf2.Variant.format() raises KeyError (not None) when the field is absent from the header. In OA-only mode all variants come from SAGE which has no SQ field. Check the header once before iterating and skip the SQ path entirely when absent — SAGE QUAL values pass through unchanged. Also close VCF handles explicitly to flush bgzip output.
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Conflicts resolved by taking oa-only-v2 content (superset of main): - CHANGELOG.md, constants.py, pcgr.py, report.py, test_pcgr_hypermutated.py
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Summary
SQFORMAT field, etc).oa-onlybranch, which drives sash's OA-only pipeline mode against these container builds.Related