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Mbs output#1376

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WardDeb merged 11 commits into4.0.0deeptools/deepTools:4.0.0from mbs_outputdeeptools/deepTools:mbs_outputCopy head branch name to clipboardJan 29, 2025

+1,620-1,341

Commits

Commits on Jan 22, 2025

• having npz output, count output if needed

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  20377d2

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Commits on Jan 24, 2025

• bins/regions implementation for multibamsummary, npz output. Implement RegionBlocks to balance number of temp files versus bps to process.

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• Include the regionblocks even if the total genome is < 1 million

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• infer bed/gtf from the first proper dataline. Escape some warnings

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• Include intersection of all chromosomes over all bam files, not crash if they are not all matching.

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Commits on Jan 25, 2025

• for regions in mbs same idea, only contain chroms that are present in header of all bam files.

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Commits on Jan 27, 2025

• simplify and include a parallel block iterator in binsize>1 calcs

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• drop the bridge par

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Commits on Jan 28, 2025

• drop v3 print statements

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• drop validchrom printing, sort regions to have proper bw files.

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Commits on Jan 29, 2025

• properly calculate mbs - BED mode

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