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Fixes to BLAST functionality and refactoring #39

Merged
merged 17 commits into from
May 7, 2024
Merged

Fixes to BLAST functionality and refactoring #39

merged 17 commits into from
May 7, 2024

Commits on Apr 30, 2024

  1. Some refactoring and fixes 

    Issues addressed here:
- Off-target amplicons are now reported as intended in the logs
- Off-target amplicons are now always considered last for the final
  scheme (no penalty is used, but the fact that they had BLAST matches
gets recorded)
- Amplicon numbering proceeds from 5' to 3' even across pools
- In the primer bed file, primers are now ordered according to the
  amplicon number without taking the pool into account

For this, the internal representation of amplicon schemes had to be
unified across the different modes and steps of the analysis.
    @wm75
    wm75 committed Apr 30, 2024
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Commits on May 1, 2024

  1. Fix amplicon sorting 

    This ensures that the best amplicons get the lowest ID numbers in the
written scheme.
    @wm75
    wm75 committed May 1, 2024
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  2. Document scheme structure as comment

    @wm75
    wm75 committed May 1, 2024
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Commits on May 2, 2024

  1. Weigh amplicon graphs by (offset_targets, costs)

    @wm75
    wm75 committed May 2, 2024
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Commits on May 3, 2024

  1. Fix sorting without blast results

    @wm75
    wm75 committed May 3, 2024
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  2. Fix same error for qPCR mode

    @wm75
    wm75 committed May 3, 2024
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  3. Fix typo which messed up sorting of amplicons in single mode

    @wm75
    wm75 committed May 3, 2024
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  4. Optimize amplicon overlap calculations and fix off-by-one errors 

    ... in all interval clculations
    @wm75
    wm75 committed May 3, 2024
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  5. Remove BLAST_PENALTY and clean up blast-related code

    @wm75
    wm75 committed May 3, 2024
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  6. Remove debug print and early return

    @wm75
    wm75 committed May 3, 2024
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  7. Sort by position within qpcr primer sets and clean up

    @wm75
    wm75 committed May 3, 2024
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  8. Write amplicons as proper bed6

    @wm75
    wm75 committed May 3, 2024
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  9. Indicate minor version

    @wm75
    wm75 committed May 3, 2024
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  10. Better use . instead of + for amplicon strand 

    Amplicons do not really sit on any single strand.
    @wm75
    wm75 committed May 3, 2024
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Commits on May 6, 2024

  1. Include off-target information in primer tsv files

    @wm75
    wm75 committed May 6, 2024
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Commits on May 7, 2024

  1. Fix primer dimer handling broken by previous changes

    @wm75
    wm75 committed May 7, 2024
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  2. Remove unused function param / arg pair

    @wm75
    wm75 committed May 7, 2024
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