Update fibertools-rs to 0.13.x and v0.2.0 housekeeping - #61
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ft pileup no longer takes the region as a positional argument, so pass it via --rgn. samtools/htslib 1.21 and bedtools 2.31.1 are required to get builds compatible with the libzlib>=1.3.2 that ft 0.12 links. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…guards Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- exclude_from_shuffle: guard empty EXCLUDES (non-hg38 refs) and use gunzip -cf instead of less for portable plain/gzip handling - pixi: skip test-data download when already present, add test-clean, start test runs from a clean state, fill in description, bump to 0.2.0 - CI: setup-pixi action v0.8.1 -> v0.9.6 - CHANGELOG for v0.2.0; ruff formatting in two scripts Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
FIRE peaks now require >=10% of reads accessible on top of FDR peak calling by default; set min_frac_accessible: 0.0 for the old behavior. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
0.12.0 has a bug where ft fire --extract reports FDR=1.0 for every MSP (fixed upstream in fibertools-rs#121); wait for the 0.13 release rather than 0.12.1. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Summary
>=0.13,<0.14) inworkflow/envs/env.yaml(with samtools==1.21, htslib==1.21, bedtools==2.31.1, needed for libzlib ≥1.3.2 compatibility)ft pileupregion arguments changed from positional to--rgn(the only CLI break since 0.6; all otherftcall sites verified compatible with 0.13)min_frac_accessiblenow defaults to 0.10: peaks must have ≥10% of reads accessible in addition to FDR peak calling (set to 0.0 for the old behavior)exclude_from_shufflenow works when noexcludesare configured (non-hg38 references), and usesgunzip -cfinstead oflessfor portable plain/gzip handlingtest-cleantask, start test runs from a clean state, version bump 0.1.2 → 0.2.0 (note: output dirs become-v0.2-)setup-pixiaction → v0.9.6Closes #54. Supersedes #55 (ports its remaining changes).
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