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Improved mapping #344

Merged
merged 12 commits into from
Dec 11, 2023
Merged

Improved mapping #344

merged 12 commits into from
Dec 11, 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

    @leoisl
    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
    @leoisl
    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

    @leoisl
    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

    @leoisl
    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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