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Sync dev to master, preparing for release 0.12.0-alpha.0 #354

Merged
merged 27 commits into from
Dec 14, 2023
Merged

Sync dev to master, preparing for release 0.12.0-alpha.0 #354

merged 27 commits into from
Dec 14, 2023

Commits on Aug 2, 2023

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Commits on Aug 3, 2023

  1. Changing the way we detect conflicts from interval envelopment to ove…

    …rlap
    
    if a cluster overlaps another by >=80%, then we detect conflict and has to filter one out
    leoisl committed Aug 3, 2023
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  5. Fixing SAM file issue

    leoisl committed Aug 3, 2023
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Commits on Aug 8, 2023

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  3. Removing redundant commentary

    leoisl committed Aug 8, 2023
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Commits on Nov 2, 2023

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Commits on Dec 11, 2023

  1. Merge pull request #344 from leoisl/improved_mapping

    Improved mapping
    leoisl authored Dec 11, 2023
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Commits on Dec 12, 2023

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  2. Merge pull request #351 from leoisl/min_gene_coverage_proportion

    feat: adds parameter --min-gene-coverage-proportion to pandora map, compare and discover
    leoisl authored Dec 12, 2023
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  3. Adding flag --no-gene-coverage-filtering to pandora map, discover and…

    … command subcommands
    leoisl committed Dec 12, 2023
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Commits on Dec 13, 2023

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  2. Merge pull request #352 from leoisl/no-gene-cov-filter

    feat: adds flag --no-gene-coverage-filtering to pandora map, compare and discover
    leoisl authored Dec 13, 2023
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  4. feat: adding param --partial-matching-lower-bound to pandora map, dis…

    …cover and command subcommands
    leoisl committed Dec 13, 2023
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  5. Merge pull request #353 from leoisl/lower_fraction_kmers_required_for…

    …_cluster
    
    feat: adding param --partial-matching-lower-bound to pandora map, discover and command subcommands
    leoisl authored Dec 13, 2023
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