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Refactoring #326

Merged
merged 18 commits into from
Aug 21, 2023
Merged

Refactoring #326

merged 18 commits into from
Aug 21, 2023

Commits on Jul 23, 2023

  1. Rename Alignment::aln_length to length

    @marcelm
    marcelm committed Jul 23, 2023
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  2. Get rid of unused Alignment::aln_score

    @marcelm
    marcelm committed Jul 23, 2023
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  3. Rename Alignment::sw_score to score

    @marcelm
    marcelm committed Jul 23, 2023
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  4. Rename Alignment::ed to edit_distance

    @marcelm
    marcelm committed Jul 23, 2023
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  5. Use more accurate types that reflect the SAM spec 

    - FLAG: 16 bits, unsigned
- POS: 32 bits, unsigned
- MAPQ: 8 bits, unsigned
- PNEXT: 32 bits, unsigned
- TLEN: 32 bits, signed
    @marcelm
    marcelm committed Jul 23, 2023
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  6. Rename all_nams to nams

    @marcelm
    marcelm committed Jul 23, 2023
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  7. Rename n to nam 

    ... wherever it is an instance of Nam
    @marcelm
    marcelm committed Jul 23, 2023
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Commits on Aug 21, 2023

  1. Rename ..._s to _start and ..._e to _end 

    In Nam and Hit structs
    @marcelm
    marcelm committed Aug 21, 2023
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  2. Rename mapping_params to MappingParameters

    @marcelm
    marcelm committed Aug 21, 2023
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  3. Rename R to rescue_level 

    in MappingParameters and in CommandLineOptions
    @marcelm
    marcelm committed Aug 21, 2023
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  4. Rename maxTries attributes to max_tries

    @marcelm
    marcelm committed Aug 21, 2023
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  5. Rename "sam_aln" to "alignment"

    @marcelm
    marcelm committed Aug 21, 2023
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  6. Rename more

    @marcelm
    marcelm committed Aug 21, 2023
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  7. Get rid of a sign-compare warning

    @marcelm
    marcelm committed Aug 21, 2023
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  8. Move get_alignment_unused() to unused.cpp

    @marcelm
    marcelm committed Aug 21, 2023
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  9. Complain if -M argument is less than one

    @marcelm
    marcelm committed Aug 21, 2023
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  10. Rename dropoff to dropoff_threshold

    @marcelm
    marcelm committed Aug 21, 2023
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  11. Rename sam_aln to alignment

    @marcelm
    marcelm committed Aug 21, 2023
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