All pull requests

Pull requests

• Keep records with conflicting mod probabilities; fix pileup on PacBio (Jasmine) tags

  #720·ljwharbers opened Sep 2, 2026·

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• Handle CRAM references, empty thresholds, and zero-target extract inputs

  #713·SuhasSrinivasan opened Aug 10, 2026·

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  3

• Correct entropy state, motif ownership, and regional statistics

  #712·SuhasSrinivasan opened Aug 10, 2026·

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• Correct repair matching, ordering, and atomic output

  #711·SuhasSrinivasan opened Aug 10, 2026·

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• Preserve independent MM-group calls and support larger code sets

  #709·SuhasSrinivasan opened Aug 10, 2026·

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• Make modification-code ordering traits consistent

  #707·SuhasSrinivasan opened Aug 10, 2026·

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• Prevent interval endpoint overflow and remove stray adjust-mods stderr output

  #706·SuhasSrinivasan opened Aug 10, 2026·

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• Make indexed sampling and threshold caps deterministic

  #705·SuhasSrinivasan opened Aug 6, 2026·

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• Correct DMR site statistics and segmentation completeness

  #704·SuhasSrinivasan opened Aug 6, 2026·

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• Correct pileup motif ownership, validation, and mask limits

  #702·SuhasSrinivasan opened Aug 6, 2026·

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• Propagate probability sampling failures

  #701·SuhasSrinivasan opened Aug 6, 2026·

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• Correct Localize coordinates, coverage, validation, and charts

  #700·SuhasSrinivasan opened Aug 6, 2026·

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• Correct Summary population and deterministic reporting

  #699·SuhasSrinivasan opened Aug 6, 2026·

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• Correct extract motif metadata and output accounting

  #698·SuhasSrinivasan opened Aug 6, 2026·

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• Propagate text and DMR output failures

  #697·SuhasSrinivasan opened Aug 6, 2026·

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• Apply edge filters consistently during probability sampling

  #696·SuhasSrinivasan opened Aug 6, 2026·

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• Pin hts-sys to bindings compatible with rust-htslib 0.46

  #666·SuhasSrinivasan opened Aug 6, 2026·

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• Validate bedMethyl merge inputs and preserve row identities

  #664·SuhasSrinivasan opened Aug 6, 2026·

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• Map bedMethyl intervals and strands into genomic space

  #662·SuhasSrinivasan opened Aug 6, 2026·

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• Correct validate truth parsing and observation accounting

  #659·SuhasSrinivasan opened Aug 6, 2026·

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• Correct pileup record state and count accounting

  #656·SuhasSrinivasan opened Aug 6, 2026·

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• Allow N

  #597·killercup opened Mar 19, 2026·

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  4

• Reservoir sampling for high-depth pileup

  #588·stein-andrew opened Feb 28, 2026·

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  1