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refactor: extract configuration, remove dead code #426

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Closed

refactor: extract configuration, remove dead code #426

wants to merge 62 commits into from

Commits on Apr 23, 2024

  1. Start extracting cellranger-related args.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  2. Start extracting the CR subset of args into a type.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  3. Remove unused bug reports config.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  4. Move the nopager config option.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  5. Remove dead NOPRETTY arg and fix up NOPAGER.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  6. Remove pager function from enclone_ranger.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  7. Restore NOPAGER proc.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  8. Remove NOPAGER from required args.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  9. Extract the PROTO arg.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  10. Extract the PROTO_METADATA arg.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  11. Mark proto/etc as done.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  12. Move NUMI into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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  13. Move NUMI_RATIO into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 23, 2024
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Commits on Apr 29, 2024

  1. Move NUMI_RATIO into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  2. Make a note that NOPRINT is unused in enclone_ranger.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  3. Move REF into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  4. Move PRE= into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  5. Make a note that internal_run is hardcoded in enclone_ranger.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  6. Make a note about refactoring how we handle MAX_CORES.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  7. Mark NUMI and NUMI_RATIO as complete.

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    macklin-10x committed Apr 29, 2024
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  8. Move FATE_FILE into cr_opts.

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    macklin-10x committed Apr 29, 2024
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  9. Move GAMMA_DELTA into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  10. Move NGRAPH_FILTER into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  11. Move NWEAK_CHAINS into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  12. Move NFOURSIE_KILL into cr_opts.

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    macklin-10x committed Apr 29, 2024
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  13. Move NDOUBLET into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  14. Move NSIG into cr_opts.

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    macklin-10x committed Apr 29, 2024
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  15. Move META into cr_opts.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  16. Tweak docstring.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  17. Delete unused cr_version param.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  18. Remove dead WEAK option.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  19. Remove unused EXP argument.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  20. Remove never-read extc param.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  21. Remove never-completed EXT functionality.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  22. Delete dead FB_SHOW arg.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  23. Remove several more dead args.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  24. Delete dead condition field in PlotOpt.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  25. Delete PLOT2 arg which has identical function as PLOT.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  26. Delete unused fields from AlleleData.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  27. Delete unused JoinAlgOpt field.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  28. Delete always-false/dead fails_only param and branch.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  29. Delete dead chain_brief option.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  30. Remove unused AG_DIST_FORMULA parameter.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  31. Remove dead vj_refname_strong parameter.

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    macklin-10x committed Apr 29, 2024
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  32. Move nogray into clono_print_opts.

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    macklin-10x committed Apr 29, 2024
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  33. Move more printing options into ClonoPrintOpt.

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    macklin-10x committed Apr 29, 2024
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  34. Remove never-read pathlist and last_modified params.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  35. Remove all code that populated dead pathlist.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  36. Remove unused loading/storing of feature_refs.

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    macklin-10x committed Apr 29, 2024
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  37. Rip out entirely-unused metrics loading code.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  38. Add validation for readability/writability.

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    macklin-10x committed Apr 29, 2024
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  39. Restore handling of FORCE_EXTERNAL.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  40. Extract SHM indel conditional.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  41. Lift graph filter conditionals.

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    macklin-10x committed Apr 29, 2024
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  42. Lift another config option out of a helper function.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  43. Lift cross filter args.

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    macklin-10x committed Apr 29, 2024
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  44. Lift barcode reuse conditional.

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    macklin-10x committed Apr 29, 2024
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  45. Start working over exact clonotype code.

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    macklin-10x committed Apr 29, 2024
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  46. Clean up exact clonotype finding.

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    macklin-10x committed Apr 29, 2024
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  47. Use an iterator to compute max_exact.

    @macklin-10x
    macklin-10x committed Apr 29, 2024
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  48. Add PRE= debug log.

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    macklin-10x committed Apr 29, 2024
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  49. Remove debug.

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    macklin-10x committed Apr 29, 2024
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