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start extracting a cellranger-only configuration subset #421

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start extracting a cellranger-only configuration subset #421

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macklin-10x
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@macklin-10x macklin-10x commented Apr 18, 2024 •
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  • Extracts most config parameters set by cellranger into a separate config struct.
  • Works over defs.rs, removing many unused or unread fields and CLI args.

macklin-10x
macklin-10x commented Apr 18, 2024
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enclone/src/misc1.rs
// Linux.

#[cfg(not(target_os = "windows"))]
pub fn setup_pager(pager: bool) {
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This code was moved into enclone proper.

@macklin-10x macklin-10x marked this pull request as ready for review April 18, 2024 22:00
@macklin-10x macklin-10x mentioned this pull request Apr 18, 2024
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@macklin-10x macklin-10x force-pushed the macklin/extract-all-enclone-only-print-code branch from 8bbdb40 to 190578b Compare April 20, 2024 02:48
@macklin-10x macklin-10x force-pushed the macklin/clean-up-cli-arg-handling branch from 8d956f9 to 4668164 Compare April 20, 2024 03:00
Base automatically changed from macklin/extract-all-enclone-only-print-code to main April 23, 2024 03:00
@macklin-10x
Start extracting cellranger-related args.
f3fd110
@macklin-10x
Start extracting the CR subset of args into a type.
7a216f2
@macklin-10x
Remove unused bug reports config.
e7b2789
@macklin-10x
Move the nopager config option.
59629ad
@macklin-10x
Remove dead NOPRETTY arg and fix up NOPAGER.
1af6d20
@macklin-10x
Remove pager function from enclone_ranger.
f992b77
@macklin-10x
Restore NOPAGER proc.
a25e9ac
@macklin-10x
Remove NOPAGER from required args.
9fe7093
@macklin-10x
Extract the PROTO arg.
1d7ccbc
@macklin-10x
Extract the PROTO_METADATA arg.
53c577a
@macklin-10x
Mark proto/etc as done.
935beee
@macklin-10x
Move NUMI into cr_opts.
0f7d07c
@macklin-10x
Move NUMI_RATIO into cr_opts.
96a71e1
@macklin-10x
Move NUMI_RATIO into cr_opts.
2282461
@macklin-10x
Make a note that NOPRINT is unused in enclone_ranger.
14e09a4
@macklin-10x
Move REF into cr_opts.
76c1345
@macklin-10x
Move PRE= into cr_opts.
2076750
@macklin-10x
Make a note that internal_run is hardcoded in enclone_ranger.
d8f0a06
@macklin-10x
Make a note about refactoring how we handle MAX_CORES.
3f56dbe
@macklin-10x
Mark NUMI and NUMI_RATIO as complete.
b460362
@macklin-10x
Move FATE_FILE into cr_opts.
43da902
@macklin-10x
Move NSIG into cr_opts.
fa80625
@macklin-10x
Move META into cr_opts.
786eebc
@macklin-10x
Tweak docstring.
f6c0a9a
@macklin-10x
Delete unused cr_version param.
e4a7e86
@macklin-10x
Remove dead WEAK option.
cbcca5e
@macklin-10x
Remove unused EXP argument.
93d0a0f
@macklin-10x
Remove never-read extc param.
6e8cc48
@macklin-10x
Remove never-completed EXT functionality.
cca0fc1
@macklin-10x
Delete dead FB_SHOW arg.
b99ee83
@macklin-10x
Remove several more dead args.
917a6a7
@macklin-10x
Delete dead condition field in PlotOpt.
f230ed2
@macklin-10x
Delete PLOT2 arg which has identical function as PLOT.
fc30b6a
@macklin-10x
Delete unused fields from AlleleData.
5ed6099
@macklin-10x
Delete unused JoinAlgOpt field.
653db37
@macklin-10x
Delete always-false/dead fails_only param and branch.
028b066
@macklin-10x
Delete dead chain_brief option.
5a4f932
@macklin-10x
Remove unused AG_DIST_FORMULA parameter.
7bd3de7
@macklin-10x
Remove dead vj_refname_strong parameter.
c15f9b0
@macklin-10x
Move nogray into clono_print_opts.
34c79dd
@macklin-10x
Move more printing options into ClonoPrintOpt.
aaec17b
@macklin-10x
Remove never-read pathlist and last_modified params.
a9033ac
@macklin-10x
Remove all code that populated dead pathlist.
9f5584f
@macklin-10x
Remove unused loading/storing of feature_refs.
319e8a8
@macklin-10x
Rip out entirely-unused metrics loading code.
ec6e76a
@macklin-10x
Add validation for readability/writability.
7c4df1f
@macklin-10x
Restore handling of FORCE_EXTERNAL.
1f4f0d7
@macklin-10x macklin-10x force-pushed the macklin/clean-up-cli-arg-handling branch from 4668164 to 1f4f0d7 Compare April 23, 2024 03:43
@macklin-10x macklin-10x marked this pull request as draft April 29, 2024 17:53
@macklin-10x macklin-10x deleted the macklin/clean-up-cli-arg-handling branch April 30, 2024 21:38
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@sreenathkrishnan sreenathkrishnan Awaiting requested review from sreenathkrishnan

@nmmsv10x nmmsv10x Awaiting requested review from nmmsv10x

@shamoni shamoni Awaiting requested review from shamoni

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