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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>
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)
When select_pcgr_variants cannot bring the PASS count below MAX_SOMATIC_VARIANTS via tiered filtering it raises RuntimeError, aborting the entire report step. This left sash with no usable SMLV_SOMATIC_REPORT output for samples with very high variant counts (e.g. L2100242 with 595,416 PASS variants — high CNA complexity, not a true hypermutator). Catch the RuntimeError, log a warning, and skip prepare_vcf_somatic and run_somatic. Non-PCGR outputs (bcftools stats, AF distributions, variant counts) continue to publish. Companion sash change marks the PCGR emits as optional. Refs: umccr/sash#52
Add three tests: - select_pcgr_variants raises RuntimeError when all SAGE_HOTSPOT variants (RETAIN_FIELDS) make tiered filtering impossible - entry() skips prepare_vcf_somatic + run_somatic when the RuntimeError is caught (core of the sash #52 fix) - entry() calls run_somatic normally when count is within the limit (regression guard)
PCGR writes PCGR_MUTATION_HOTSPOT=. (Type=String placeholder) on every non-hotspot variant. cyvcf2 returns the string '.' which Python evaluates as truthy, so any(variant.INFO.get(e) ...) always returned True — ALL variants were treated as retained, variants_sorted stayed empty, and select_pcgr_variants raised RuntimeError for any sample with >450k PASS variants (sash #52 root cause). Fix: exclude '.' alongside None so only genuinely set String/Flag fields trigger retention. Adds regression test with PCGR_MUTATION_HOTSPOT=. fixture to prevent silent recurrence.
* fix: drop --estimate_signatures from PCGR somatic invocation PCGR's mutational signature estimation is unreliable for our cohort and we get signature analysis from gpgr/sigrap downstream. Keep --estimate_msi and --estimate_tmb (still useful in the PCGR report). Refs: umccr/sash#57 * Apply suggestions from code review Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Documents CI smoke tests, build fixes, split_vcf tabix-indexing, r-gpgr 2.3.1 bump, and the estimate_signatures drop (#31, sash#57) — all merged into release/0.3.0 after the v0.3.1 tag but never recorded.
* fix: skip PCGR when variant count exceeds MAX_SOMATIC_VARIANTS When select_pcgr_variants cannot bring the PASS count below MAX_SOMATIC_VARIANTS via tiered filtering it raises RuntimeError, aborting the entire report step. This left sash with no usable SMLV_SOMATIC_REPORT output for samples with very high variant counts (e.g. L2100242 with 595,416 PASS variants — high CNA complexity, not a true hypermutator). Catch the RuntimeError, log a warning, and skip prepare_vcf_somatic and run_somatic. Non-PCGR outputs (bcftools stats, AF distributions, variant counts) continue to publish. Companion sash change marks the PCGR emits as optional. Refs: umccr/sash#52 * test: cover PCGR graceful skip on unresolvable variant count overflow Add three tests: - select_pcgr_variants raises RuntimeError when all SAGE_HOTSPOT variants (RETAIN_FIELDS) make tiered filtering impossible - entry() skips prepare_vcf_somatic + run_somatic when the RuntimeError is caught (core of the sash #52 fix) - entry() calls run_somatic normally when count is within the limit (regression guard) * fix: treat PCGR_MUTATION_HOTSPOT=. as missing in retention check PCGR writes PCGR_MUTATION_HOTSPOT=. (Type=String placeholder) on every non-hotspot variant. cyvcf2 returns the string '.' which Python evaluates as truthy, so any(variant.INFO.get(e) ...) always returned True — ALL variants were treated as retained, variants_sorted stayed empty, and select_pcgr_variants raised RuntimeError for any sample with >450k PASS variants (sash #52 root cause). Fix: exclude '.' alongside None so only genuinely set String/Flag fields trigger retention. Adds regression test with PCGR_MUTATION_HOTSPOT=. fixture to prevent silent recurrence. * refactor: tighten retention-check comment to one line * test: assert real PCGR_MUTATION_HOTSPOT value retains variant
…ogger.info cleanup
Graceful PCGR skip when variant count exceeds MAX_SOMATIC_VARIANTS (sash #52, bolt PR #32). Fixes dot-placeholder PCGR_MUTATION_HOTSPOT retention false positive. Approved by scwatts (2026-06-05), all CI green.
Drops comments that restate what the code already says (logger setup, execute_command flag explanation, merge step annotations) and replaces multi-paragraph docstrings on merge_tsv_files/merge_vcf_files with no docstring, per project conventions.
This was referenced Jul 17, 2026
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Closing — redundant with bolt #33 which already covers the full release/0.3.0 tip including 0.3.2. Created in error. |
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Release 0.3.2
Merges bolt 0.3.2 into
main. Builds on bolt #35 (release/0.3.1-validated→main, 0.3.0 + 0.3.1) — merge that first.Fixed
MAX_SOMATIC_VARIANTS— graceful skip, non-PCGR outputs still publish (#32, sash #52)PCGR_MUTATION_HOTSPOT=.treated as truthy in retention check — was blocking tiered filtering for any sample with >450k PASS variants (#32)--estimate_signaturesfrom PCGR somatic invocation — signature analysis is downstream in gpgr/sigrap (#31, sash #57)--estimate_msi/--estimate_tmbin chunked PCGR annotation runs — estimates on partial VCFs are not meaningfuljlumbroso/free-disk-spaceCI action tov1.3.0Tests added
TestRunSomaticCommandArgs(estimate flags),TestEntrySkipsPcgrOnOverflow,TestSelectPcgrVariantsRaisesOnUnresolvableOverflow,disable_estimatesforwarding inTestRunSomaticChunkArgMappingPrerequisite