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Commits on Jan 19, 2026

• Merge branch 'ar/prep-061' into 'master'

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• Prep 061

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Commits on Jan 18, 2026

• Merge branch 'ar/docs-tweak' into 'master'

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• Docs tweak

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• Prep 061 docs

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• Fix high depth overflow, add `--high-depth`

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• feat(motif): changes motif comparison logic to compare sequence spaces.

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• fix(pileup): bgzf-compression with general multiple motifs

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• fix(modbam, adjust-mods): add CG 0 when `--cpg` flag is passed.

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• Use default threshold for unmentioned bases.

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• fix(pileup): emit only 5hmC records with `--modified-bases 5hmC`

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• Fix typo

  

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• test(pileup): add test that phased combined is the same as unphased

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• fix(pileup): correct stride when only one modification is given in --phased mode

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• chore: bump version to 0.6.1

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• fix(pileup, generic): actually use combine-strands with generic workers.

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• Merge pull request #535 from WardDeb/master

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Commits on Nov 30, 2025

• Merge branch 'ar/modified-bases-docstring' into 'master'

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• docs(pileup): adds doc string for `--modified-bases`

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• Merge branch 'ar/chore-build-docs-060' into 'master'

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• chore(docs): build docs

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• Merge branch 'ar/docs-fixes-060' into 'master'

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• docs(readme, online): tweaks to language.

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• Merge branch 'ar/prep-060' into 'master'

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• Prep 060

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• Merge branch 'ar/modbam-subcommands' into 'master'

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• chore(modbam): move modbam commands into subcommand

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• Merge branch 'ar/new-pileup-algo' into 'master'

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• [v0.6.0] Refactor pileup

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Commits on Nov 7, 2025

• allow header in bedmethyl files for bigwig creation

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• fix source install from path

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Commits on Sep 11, 2025

• Merge branch 'ar/changelog-051rc1' into 'master'

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• Prepare docs 0.5.1-rc1

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• Merge branch 'ar/gh451' into 'master'

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• refactor(dmr, regions): makes effect sizes exp - control.

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