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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

  1. Now filtering clusters based on the read span length of the hits

    @leoisl
    leoisl committed Aug 2, 2023
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  2. Now preferring clusters with higher number of unique minimisers

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    leoisl committed 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
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    leoisl committed Aug 3, 2023
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  2. Placeholder for POS in SAM file is now 1, so that is compliant with f… 

    …ormat
    @leoisl
    leoisl committed Aug 3, 2023
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  3. Refactoring prg_min_path_lengths -> prg_max_path_lengths

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    leoisl committed Aug 3, 2023
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  4. Now using target coverage to untie equally good mappings

    @leoisl
    leoisl committed Aug 3, 2023
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  5. Fixing SAM file issue

    @leoisl
    leoisl committed Aug 3, 2023
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  6. Now adding a tolerance when comparing the nb of unique minimisers from 

    different clusters
    @leoisl
    leoisl committed Aug 3, 2023
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Commits on Aug 8, 2023

  1. Adding CLI param --min-cluster-overlap

    @leoisl
    leoisl committed Aug 8, 2023
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  2. Adding parameter --cluster-mini-tolerance

    @leoisl
    leoisl committed Aug 8, 2023
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  3. Removing redundant commentary

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

  1. Merge branch 'dev' into improved_mapping

    @leoisl
    leoisl committed Nov 2, 2023
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  2. Adding parameter min_gene_coverage_proportion to LocalPRG::add_consen… 

    …sus_path_to_fastaq()
    @leoisl
    leoisl committed Nov 2, 2023
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  3. Adding --min-gene-coverage-proportion CLI arg to the discovery subcom… 

    …mand
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    leoisl committed Nov 2, 2023
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  4. Adding --min-gene-coverage-proportion CLI arg to the compare subcommand

    @leoisl
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  5. Adding --min-gene-coverage-proportion CLI arg to the map subcommand

    @leoisl
    leoisl committed Nov 2, 2023
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  6. Fixing default value for max_relative_gene_coverage for the discovery… 

    … subcommand
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    leoisl committed Nov 2, 2023
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Commits on Dec 11, 2023

  1. Merge pull request #344 from leoisl/improved_mapping 

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

  1. refactor: removing debugging log message

    @leoisl
    leoisl committed 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
    leoisl authored Dec 12, 2023
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  3. Adding flag --no-gene-coverage-filtering to pandora map, discover and… 

    … command subcommands
    @leoisl
    leoisl committed Dec 12, 2023
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  4. fix: fix a typo in --no-gene-coverage-filtering CLI help

    @leoisl
    leoisl committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. fix: solving issues with rebasing on dev

    @leoisl
    leoisl committed 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
    leoisl authored Dec 13, 2023
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  3. Lowering fraction_kmers_required_for_cluster to allow for 10% partial… 

    … matches
    @leoisl
    leoisl committed Dec 13, 2023
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  4. feat: adding param --partial-matching-lower-bound to pandora map, dis… 

    …cover and command subcommands
    @leoisl
    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
    leoisl authored Dec 13, 2023
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