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Add --exclude-low-support and --convergence-criterion flags - #45

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marco-cominelli01 merged 6 commits into
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EM_updates
Apr 16, 2026
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Add --exclude-low-support and --convergence-criterion flags#45
marco-cominelli01 merged 6 commits into
mainfrom
EM_updates

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@marco-cominelli01 marco-cominelli01 commented Mar 26, 2026

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  • Add optional flag --exclude-low-support to filter out features supported only by 1 multi-mapping UMI and no uniquely mapped UMIs prior EM optimization, improving performance without significantly affecting results.
  • Add flag --convergence-criterion to base EM convergence on either log-likelihoods or estimates (using the latter speeds up EM convergence at the cost of precision). Defaults on log-likelihood.

@bepoli bepoli changed the title Add filter for unreliable features and additional convergence criterion Add --exclude-low-support and --convergence-criterion flags Apr 15, 2026
@bepoli bepoli added the enhancement New feature or request label Apr 15, 2026
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bepoli self-requested a review April 15, 2026 15:29
@marco-cominelli01
marco-cominelli01 merged commit bd61551 into main Apr 16, 2026
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@bepoli
bepoli deleted the EM_updates branch April 16, 2026 10:38
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