Polar basecalling - #208

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jshleap wants to merge 28 commits into

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polar-basecalling

Commits on Aug 17, 2026

Support dark bases
joshua-gould
committed
70386a5
added dark base test
joshua-gould
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ed7a742
adding bernoulli independent trial strategy to bacode decoding
jshleap
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feecec2
Apply ruff formatting
jshleap
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9d0bc0c

Commits on Aug 19, 2026

Changing f estimation and adjusting normalization
jshleap
committed
4f1bb16

Commits on Aug 20, 2026

Add polar-coordinate basecaller (decode_polar)
jshleap
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87a6f78
adding notebook, and ruff edits
jshleap
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48df0b0
adding notebook, missed the addd before
jshleap
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9dd2dd1

Commits on Aug 21, 2026

Commits on Aug 26, 2026

Reverting CLI and main flow changes, and adding independent function for SE (polar was already independent)
jshleap
committed
4bd5aef

Commits on Aug 27, 2026

Reverted to main
joshua-gould
committed
3ba3c41
Merge branch 'main' of https://github.com/Genentech/scallops into polar-basecalling
joshua-gould
committed
8f209d8
Reverted
joshua-gould
committed
02a965f
Removed unused
joshua-gould
committed
468046e
Added example data
joshua-gould
committed
2c67577
Merge branch 'main' of https://github.com/Genentech/scallops into polar-basecalling
joshua-gould
committed
933d3ce
chaning path of experimentc cells
jshleap
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8c68af7
Merge remote-tracking branch 'origin/polar-basecalling' into polar-basecalling
jshleap
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f51e116
Switching notebook and test to use the raw tiles intead of npy
jshleap
committed
a6999e5

Commits on Aug 28, 2026

Merge branch 'main' of https://github.com/Genentech/scallops into polar-basecalling
joshua-gould
committed
1c4c16c

Commits on Aug 31, 2026

merging main
jshleap
committed
48db79c
adding direct comparison notebook and adjusting tests
jshleap
committed
6b205e6
updating notebook
jshleap
committed
28f5720

Commits on Sep 9, 2026

Commits on Sep 11, 2026

Use random seed for selecting reads for decode_polar.
joshua-gould
committed
65e8cb1