deeptools/deepTools: 4.0.0

Le résumé fourni par la source

What's Changed new Rust-backed core for bamCoverage, bamCompare, computeMatrix, alignmentSieve and multiBamSummary (rayon multithreading, bigtools-based bigWig I/O), replacing the pure-Python implementations for these five tools; the previous Python implementations remain available as bamCoverage_old, bamCompare_old, computeMatrix_old, alignmentSieve_old and multiBamSummary_old during the transition, but will be removed in a future release gzipped GTF/BED region files are now supported in multiBamSummary, computeMatrix and alignmentSieve; gzipped blacklist files are supported in all five Rust-backed tools (multiBamSummary, computeMatrix, alignmentSieve, bamCompare, bamCoverage) --exactScaling is removed as this is the only scaling option available with the new backend --ignoreDuplicates has been removed from the bamCoverage and bamCompare tools. Duplicate reads can be removed via the --samFlagExclude option (assuming the provided BAM file has duplicate reads marked) plotPCA re-implemented with a lightweight scipy/numpy SVD backend. Proper handling of --transpose, --log2/--rowCenter and --ntop options. plotly backend removed entirely; plotCorrelation, plotPCA, plotHeatmap, plotProfile and plotEnrichment now use matplotlib, with a new optional --ggplot theme, and computeGCBias's --plotFileFormat plotly option has also been removed removed the standalone cm.py colormap module; colormap handling now lives in the plotting tools directly plot labels now show sample names only per default (dropped .filtered.bam/.bed suffixes) prebuilt wheels now cover Linux manylinux_2_28 and musllinux_1_2 (x86_64 + aarch64) and macOS (Intel + Apple Silicon), built via maturin CI overhauled: pytest/rust/planemo test workflows split up (test_pytest.yml, test_rust.yml, test_planemo.yml), zizmor hardening for GitHub Actions, dependabot enabled extensive new pytest/cargo test coverage across the Rust-backed tools and plotCorrelation/plotPCA/plotFingerprint data outputs --nanAfterEnd doesn't rescale the inner region anymore in reference-point mode BED output doesn't show wrong blockstart values anymore blacklist filtering is done at bp level instead of genome chunk level for rewritten tools alignmentSieve output order matches input order exactly --missingDataAsZero no longer takes bases exceeding chromosome bounds as 0 values but rather purges the bins large scale values precision slightly altered with new backend (f32 vs f64) Full Changelog: https://github.com/deeptools/deepTools/compare/3.5.6...4.0.0

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