Update main dimelo repo to v0.2.0#112
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…ling. Added quiet mode for not tracking outputs. Found that there is a performance difference in some cases: this needs to be resolved! Also, fixed a mistake in the tutorial wherein modkit_parsing_main rather than modkit_parsing_beta was referenced for Colab install.
… quiet mode, which should also look at the other printouts. Fixed tqdm imports for jupyter, need to test on command line and on Colab.
Modkit parsing oberon
Modkit parsing beta
…tebook, because ipywidgets seems to not work properly.
…it_parsing_oberon Merging recent changes from beta and my branch
Modkit parsing oberon
DM-65 Fixed mistake in utils.import_tqdm that made Colab import the J…
DM-65 Simplified tqdm importing.
DM-65 Tweaks to Colab setup in tutorial that should make progress bar…
Fixed regions=None bug. Clarified setup.py package version info.
… scope of quiet mode.
…lodon and Guppy files. Set threshold of 0.35 to throw an error and provided an override to ignore errors.
…d tutorial. Returns None is regions=None when calling the function.
…e_bam.pileup. Changed regex for run_modkit final status bar update cleanup.
Modkit parsing oberon
… Berkeley HPC Savio OOD interface and works fine on Colab too, and no problems running locally on M1 Mac.
Changed ipywidgets version from 7.7.1 to 7.6.5 because 7.6.5 works on…
Clarifications regarding Windows compatibility.
…rocessed-tests-baseline New test_matrix and cases to cover 1, 2, 3, 4, and None for cores
Feature/dm 215,dm 113,dm 90 genome browser exports, test phase 2, read depth qc
…read-plotting Dm 38 subset reads for single read plotting
…ub.com/streetslab/dimelo_v2 into feature/DM-191-refactor-load-processed
…rocessed Feature/dm 191 refactor load processed pileup
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Overhaul / rewrite to increase speed, flexibility, stability, and interoperability. Upgrade from 0.1.0 to 0.2.0 involves many substantial API changes but maintains the same core functionality.