Update main dimelo repo to v0.2.0#112

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Jun 5, 2025

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Commits on Feb 12, 2024

DM-65,DM-55,DM-57 A first pass at progress bars and modkit error handling. Added quiet mode for not tracking outputs. Found that there is a performance difference in some cases: this needs to be re…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-65 Fixed slowdown issue by updating progress bars less often. Kept quiet mode, which should also look at the other printouts. Fixed tqdm imports for jupyter, need to test on command line and on …

Oberon Dixon-Luinenburg
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Merge pull request #81 from streetslab/modkit_parsing_oberon
OberonDixon
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Merge pull request #82 from streetslab/modkit_parsing_beta
OberonDixon
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DM-65 Switching Colab tqdm back to just standard, rather than tqdm.notebook, because ipywidgets seems to not work properly.

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Oberon Dixon-Luinenburg
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Merge remote-tracking branch 'origin/modkit_parsing_oberon' into modkit_parsing_oberon

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #83 from streetslab/modkit_parsing_oberon
OberonDixon
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DM-65 Fixed mistake in utils.import_tqdm that made Colab import the Jupyter version.

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Merge pull request #84 from streetslab/modkit_parsing_oberon
OberonDixon
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DM-65 Simplified tqdm importing.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #85 from streetslab/modkit_parsing_oberon
OberonDixon
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DM-65 Tweaks to Colab setup in tutorial that should make progress bars work.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #86 from streetslab/modkit_parsing_oberon
OberonDixon
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Fixed regions=None bug. Clarified setup.py package version info.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #87 from streetslab/modkit_parsing_oberon
OberonDixon
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DM-65 Cleaned up outputs, added new h5 saving progress bars, expanded scope of quiet mode.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-13 Implemented and tested .bam reference genome checking with Megalodon and Guppy files. Set threshold of 0.35 to throw an error and provided an override to ignore errors.

Oberon Dixon-Luinenburg
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DM-48 Implemented regions.processed.bed return in pileup, extract, and tutorial. Returns None is regions=None when calling the function.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-64,DM-65 Added pileup.bed.gz.tbi to the prep_outputs call for parse_bam.pileup. Changed regex for run_modkit final status bar update cleanup.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Documentation updates.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #88 from streetslab/modkit_parsing_oberon
OberonDixon
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Changed ipywidgets version from 7.7.1 to 7.6.5 because 7.6.5 works on Berkeley HPC Savio OOD interface and works fine on Colab too, and no problems running locally on M1 Mac.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #89 from streetslab/modkit_parsing_oberon
OberonDixon
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Commits on Feb 13, 2024

Clarifications regarding Windows compatibility.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #90 from streetslab/modkit_parsing_oberon
OberonDixon
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Commits on Feb 15, 2024

Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
OberonDixon
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Update README.md
thekugelmeister
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tutorial cleanup
Oberon Dixon-Luinenburg
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Merge pull request #91 from streetslab/modkit_parsing_beta
OberonDixon
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Merge pull request #92 from streetslab/modkit_parsing_oberon
OberonDixon
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Updated dependencies to make progress bars work better on standard/local jupyter notebooks. Need to now test how to make this work still on Colab.
Oberon Dixon-Luinenburg
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Reconciling.
Oberon Dixon-Luinenburg
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Readme updates for ipywidgets versioning.
Oberon Dixon-Luinenburg
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Small updates
Oberon Dixon-Luinenburg
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Merge pull request #93 from streetslab/modkit_parsing_oberon
OberonDixon
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Added Colab ipywidgets version specifier in tutorial code and README install code block.
Oberon Dixon-Luinenburg
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small readme tweak for progress bars
Oberon Dixon-Luinenburg
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Merge pull request #94 from streetslab/modkit_parsing_oberon
OberonDixon
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tweak colab install typo
Oberon Dixon-Luinenburg
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Commits on Feb 16, 2024

Readme updates to reflect difficulties with early modkit termination and installation on HPC clusters. Tweaks to dependencies.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Feb 17, 2024

Update README.md
thekugelmeister
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Small README clarifications

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Added design objectives

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Feb 19, 2024

Merge pull request #95 from streetslab/modkit_parsing_beta
OberonDixon
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Commits on Feb 22, 2024

New comments on cores=1 parameter to resolve memory issues.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Feb 23, 2024

Merge pull request #96 from streetslab/modkit_parsing_beta
OberonDixon
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DM-99 Fixed synthetic data testing in advance of building out test workflow.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Mar 2, 2024

DM-99,DM-100 Build out pytest test cases, all 24 pass on my machine. Need to complete load_processed coverage for single reads.

Oberon Dixon-Luinenburg
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DM-99, DM-100 Deleted the old test notebook as it is not longer relevant. Fixed a silly change to the tutorial. Created a new notebook for generating test targets, and some pickles for single read …

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-100 Created a more extensible tast matrix infrastructure in the generate_test_targets notebook. dimelo_test.py currently passes all 24 tests but has not yet adapted the extensible test matrix.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Mar 3, 2024

DM-100 Moved test folder into core package to make it easier to import as dimelo.test. Updated tutorial to reflect new test data location and adjusted genome downloading in tutorial to be smoother …

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Mar 4, 2024

DM-100 Made it possible to instantiate RelativePath with an absolute path input. Adjusted generate_test_targets.ipynb to save results as well as kwargs as RelativePath objects, to fix a problem whe…
Oberon Dixon-Luinenburg
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DM-100 smaller set of tests from Savio to run on local mac.
Oberon Dixon-Luinenburg
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DM-100 Changed pileup.bed.gz output test to first decompress the file, because Linux and Mac gzipped filed are different even when using identical zlib and pysam versions. Regenerated a four-condit…

Oberon Dixon-Luinenburg
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DM-100 Added a test.yaml file that should allow us to run pytest on GitHub action runners.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-100 Changed to yml for consistency with main.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-100 Adjusted test.yml to run on dispatch OR when pushing to main or a newly specified modkit_parsing_run_tests branch. This branch doesn't exist yet but hopefully when I create it I can then run…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Small tweak

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-100 Changed the activate command back to conda activate. source was clearly the wrong thing to change this to, even though that was what the original file from main said

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Troubleshooting conda package list - why won't pytest run?

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Added conda activate commands for the different run sections, because conda list seemed to show that we aren't in the enrivonment anymore.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merged all into one run to see if that helps.

Oberon Dixon-Luinenburg
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DM-100 Working ubuntu tests via .github/workflows/test.yml. Adding macos tests to see if we can get both. Will likely keep macos tests commented out because macos servers are expensive when using G…

Oberon Dixon-Luinenburg
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DM-49 Macos and Linux tests work, rolling back Macos tests because 30min@10x cost multiple is a significant fraction of the 2000min per month free allowance. Linux tests are about 12min, we can run…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #97 from streetslab/modkit_parsing_run_tests
OberonDixon
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Commits on Mar 5, 2024

DM-117 Built the core framework but something still isn't lining up with the outputs, need to debug. Should be backwards compatible though, at least. pytest confirms.

Oberon Dixon-Luinenburg
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DM-117, DM-100 Fixed pipeline issues for recapitulating exact outputs for boolean and prob mod_vectors as part of single read compression improvement. Can now recapitulate expected values. Adjusted…
Oberon Dixon-Luinenburg
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Merge pull request #98 from streetslab/modkit_parsing_single_read_compression
OberonDixon
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DM-100 Adjust test data so that single read checking is looking at a A,0-modification-rich read. Verified that all 73 tests pass on the pre-single-read-compression version of parse_bam and load_pro…
Oberon Dixon-Luinenburg
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Merge pull request #99 from streetslab/modkit_parsing_oberon
OberonDixon
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DM-117, DM-100 further updates to test matrix to cover high methylation fraction read.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #100 from streetslab/modkit_parsing_oberon
OberonDixon
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Commits on Mar 6, 2024

Commits on Mar 7, 2024

Merge pull request #103 from streetslab/modkit_parsing_run_tests
OberonDixon
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DM-119 Made h5 loading parallel for mod and val vectors in each region, allowing us to achieve approximately the same load_processed speed as the poor compression design when looking at binarized h…

Oberon Dixon-Luinenburg
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DM-120,DM-49 Implemented chunked single read h5 writing for a greater than 10x speedup, and adjusted extract unit test to check h5 contents in a compression- and chunking-agnostic way.

Oberon Dixon-Luinenburg
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Merge pull request #104 from streetslab/modkit_parsing_single_read_compression
OberonDixon
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Merge pull request #105 from streetslab/modkit_parsing_run_tests
OberonDixon
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Commits on Mar 22, 2024

Merge pull request #1 from streetslab/modkit_parsing_oberon
thekugelmeister
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Commits on Apr 8, 2024

Fixing errors from ruff check
thekugelmeister
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Commits on Apr 9, 2024

Commits on Apr 10, 2024

Commits on Apr 13, 2024

more mypy changes
thekugelmeister
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Commits on May 8, 2024

DM-108 Added h to list of valid cytosine modifications in utils BASEMOD_NAMES_DICT, which should be referenced by default if a mod name isn't specified
Oberon Dixon-Luinenburg
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DM-142,DM-143 Adjusted parse_bam.extract, parse_bam.check_bam_format, parse_bam.read_by_base_txt_to_hdf5, and utils.DEFAULT_COLORs. plot_reads.plot_reads and parse_bam.pileup need no direct modific…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on May 9, 2024

DM-144,DM-145,DM-149 Added load_processed.pileup mod code filtering. Pileup plotters should not need any modification to work out-of-the-box.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-104 parse_bam.check_bam_format now looks for the specified mod codes and no longer throws an error if weird ones are present: instead, it warns the user and gives them instructions for adjusting…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-150 Introduced utils.ParsedMotif class to centralize motif parsing, shared across all parse_bam and load_processed functions that need to parse motifs. Plot modules only parse motifs inasmuch as…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on May 12, 2024

DM-159 Pileup counts windows, because this makes some basic checks/tests way easier, and I think in general we should have this feature. It's supported by default by all the backend infrastructure …

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-159 Rolling back pileup counts window for now, because it breaks tests and I want to keep DM-114 test changes to zero for the initial merge. DM-159 will be split out of the epic and handled at a…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #5 from streetslab/feature/DM-114-mod-names-C+h-vs-C+m
OberonDixon
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Commits on May 13, 2024

DM-155,DM-156 Added load_processed parameters single_strand for pulling out only reads for a region's strand (and omitting the other strand) and regions_5to3prime for loading all regions in the 5 p…

Oberon Dixon-Luinenburg
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DM-161 Add improved strand handling to plotting functions.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-150 Removed warning from the ParsedMotif class for now; it is really annoying to constantly get warnings about something that is fine. We can just document the default behavior well for people.

Oberon Dixon-Luinenburg
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Merge pull request #6 from streetslab/feature/DM-114-mod-names-C+h-vs-C+m
OberonDixon
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DM-162,DM-163 Added mod codes and improved strand handling to the tutorial. This is a basic first pass; we want better instructions at some point I think.

Oberon Dixon-Luinenburg
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DM-160 Fixed bug in (-) strand case for region strings.
Oberon Dixon-Luinenburg
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Merge pull request #7 from streetslab/feature/DM-154-Improved-region-strand-handling
OberonDixon
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DM-155,DM-156 Fixed a mistake regarding the bed format. Some of my test bed files had strand in the wrong place; now we look only in the right place. Confirmed working on some of Nathan's data.
Oberon Dixon-Luinenburg
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Commits on May 14, 2024

DM-164 Now regions.processed.bed never specifies strand. Updated test targets accordingly.
Oberon Dixon-Luinenburg
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Commits on May 15, 2024

browser notebook demo
thekugelmeister
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some checkpoints
Oberon Dixon-Luinenburg
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Responding to comment for https://github.com/streetslab/dimelo_v2/pull/8
Oberon Dixon-Luinenburg
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Merge pull request #8 from streetslab/feature/DM-114-mod-names-C+h-vs-C+m
OberonDixon
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Commits on May 17, 2024

DM-152 Code review with @thekugelmeister. Updated docstrings and comments, small refactors, flagged TODOs.

Oberon Dixon-Luinenburg
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Attempt to future-proof matplotlib legend handling for plot_reads

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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A few more tiny tweaks to plot_reads legend stuff

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge remote-tracking branch 'origin/main' into plot_browser_port
thekugelmeister
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Commits on May 30, 2024

Fixed downcasting warning
thekugelmeister
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Commits on May 31, 2024

Commits on Jun 5, 2024

Removing todo
thekugelmeister
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Commits on Jun 6, 2024

split top-level method into parts
thekugelmeister
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Commits on Jun 8, 2024

Commits on Jun 10, 2024

Update README.md
OberonDixon
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collapse option kwargs; improved hover text
thekugelmeister
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hover option; sane minimum gap default
thekugelmeister
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DM-31 Added plot_browser to the tutorial, along with single read extraction details and more hints for visualizations

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Added example error message for plot_browser with binarized .h5 file

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Jun 13, 2024

Merge pull request #10 from streetslab/plot_browser_port
OberonDixon
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Commits on Jun 29, 2024

DM-188 Fixed Dorado and PacBio plot_read_browser index mapping error caused by duplicate read rows in cases where read_start and read_end are off by a few bp between different motifs. This should p…
Oberon Dixon-Luinenburg
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DM-109 Return code and signal catching for modkit subprocess
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DM-165,DM-169,DM-193,DM-194 Substantial run_modkit structure changes and minor message output changes
Oberon Dixon-Luinenburg
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DM-194 Added reset for step 2 pbars once step 1 is complete, to get a more accurate initial time estimate. Fixed some structure mistakes and clarified comments

Oberon Dixon-Luinenburg
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DM-194 If statement consolidation

Oberon Dixon-Luinenburg
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DM-195 Ignore reads without sequence when checking sequence. Gives reasonable results

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Jun 30, 2024

DM-194 Move pbars into a separate function, improve comments

Oberon Dixon-Luinenburg
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Commits on Jul 1, 2024

DM-190,DM-197 Clarifying message with return code -9 and quick check in run_modkit for gzipped ref genome.

Oberon Dixon-Luinenburg
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DM-189 Check read contents for booleanized mod data before processing reads for plotting
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Commits on Jul 11, 2024

Added a comment describing empty query_sequence in some files.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Merge pull request #11 from streetslab/feature/DM-186,DM-187-modkit-monitoring-and-browser-bugfixes
OberonDixon
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Commits on Sep 15, 2024

Commits on Sep 28, 2024

Commits on Sep 29, 2024

Merge pull request #13 from streetslab/DM-209-Split-plotting-methods-into-data-retrieval-and-plot-creation
thekugelmeister
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Commits on Jan 5, 2025

DM-216 Added basic bigiwig export, and adjusted TODOs for load_processed functions to cover future plans to collapse redundant code
Oberon Dixon-Luinenburg
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DM-217 Added tests for export. Fixed some small problems in the export bigwig code. Added checkpoints to gitignore.
Oberon Dixon-Luinenburg
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Commits on Jan 6, 2025

Removed checkpoint files
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DM-218 Add test coverage for plot_read_browser, including some error cases. Added error handling for utils.parse_region_string as this is called directly by plot_read_browser rather than routing th…
Oberon Dixon-Luinenburg
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DM-218 Added a new test case to cover plot_read_browser error throwing. Adjustments to test routine and error throwing for plot_read_browser. Re-generated all test targets, after verifying that dim…
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DM-226 Pileup counts window_size logic for loading and plotting.
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DM-221 Adjust test targets pickle with new counts values given windowing
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Commits on Jan 7, 2025

DM-220 Updates to test target generator structure and test README. Test target values should be unchanged.
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Adjusted generate_targets to run from any directory by tweaking path management. Confirmed that generation and test run successfully on macos.

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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DM-227 Bigwig export cell in Advanced Use Cases section of tutorial

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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ruff format adjustments
Oberon Dixon-Luinenburg
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DM-93 Depth profile plots, including tutorial example to show that it works
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DM-230 Test coverage for plot_depth_profile; same tests as plot_enrichment_profile.
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DM-222,DM-225 Added coverage histogram module with corresponding new functions in load_processed (load region-by-region) and utils (hist plotter).
Oberon Dixon-Luinenburg
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DM-222,DM-225 Added progress bars for region-by-region loading. Added read depth histogram to __init__.
Oberon Dixon-Luinenburg
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DM-222,DM-225 Parallelization for a very substantial speedup in load_processed.regions_to_list, and thus a speedup for plot_depth_histogram functions. Added a useful little cores_available utility …
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DM-225,DM-192 Stubs to support future parallelization of load_processed core functions.
Oberon Dixon-Luinenburg
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DM-230 Adding tests for plot_depth_histogram and load_processed.regions_to_list.
Oberon Dixon-Luinenburg
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Commits on Jan 8, 2025

DM-93 Enable non-windowed profiles
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DM-229 Consolidating parsing logic for load_processed functions. Still need to apply to export functions, and need to check that performance is unimpacted.
Oberon Dixon-Luinenburg
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DM-231 Removed regions=None case for pileup_counts_from_bedmethyl because it will complicate parallelization and is not clearly useful.
Oberon Dixon-Luinenburg
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DM-229 Adjusted export.pileup_to_bigwig to use new load_processed.process_pileup_row and renamed/configured a few variables to support this.
Oberon Dixon-Luinenburg
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Commits on Jan 9, 2025

Commits on Jan 10, 2025

DM-192,DM-236 Properly close and delink shared memory when appropriate to avoid intermittent crashes. Adjust tabix fetch to avoid negative start values. Tweak wording on progress bars.
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DM-191 Re-arrange contents of load_processed for better clarity. Added some comments.
Oberon Dixon-Luinenburg
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Commits on Jan 17, 2025

Commits on Jan 18, 2025

DM-239 Adjusted generate_targets module to properly handle cores argument for extract. Updated test_matrix.pickle by re-running generate_targets. No changes to pileup or extract files, but should p…

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Ruff format fixes

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Jan 24, 2025

Added ref_genome fasta option for export contig definition. Passes tests, added to tutorial.
Oberon Dixon-Luinenburg
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Adjusted Path conversion for filepaths and added some comments.
Oberon Dixon-Luinenburg
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Fixed typo
Oberon Dixon-Luinenburg
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Commits on Jan 25, 2025

Improved docstrings and streamlined code for regions_to_list
Oberon Dixon-Luinenburg
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Documented more stuff for depth histograms.
Oberon Dixon-Luinenburg
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Added some words
Oberon Dixon-Luinenburg
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A bunch of little documentation fixes for test infra
Oberon Dixon-Luinenburg
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Further depth tweaks per PR comments
Oberon Dixon-Luinenburg
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Commits on Jan 27, 2025

Commits on Feb 21, 2025

Merge branch 'main' into feature/DM-191-refactor-load-processed
OberonDixon
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Fixed small mistakes from merge

Oberon Dixon-Luinenburg
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Oberon Dixon-Luinenburg
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Commits on Feb 26, 2025

Commits on Mar 12, 2025

Merge pull request #23 from streetslab/DM-38-Subset-reads-for-single-read-plotting
OberonDixon
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Commits on Mar 13, 2025

Merge branch 'main' into feature/DM-191-refactor-load-processed
OberonDixon
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Commits on Mar 18, 2025

Added check for chrom in tabixfile.
Oberon Dixon-Luinenburg
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Commits on Mar 23, 2025

DM-191 Adjustments in response to PR comments from thekugelmeister
Oberon Dixon-Luinenburg
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Merge branch 'feature/DM-191-refactor-load-processed' of https://github.com/streetslab/dimelo_v2 into feature/DM-191-refactor-load-processed
Oberon Dixon-Luinenburg
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Commits on May 30, 2025

Adjust naming for regions_to_list region-splitting parallelization parameter.

Oberon Dixon-Luinenburg
authored and
Oberon Dixon-Luinenburg
committed

Commits on May 31, 2025

Commits on Jun 5, 2025

Merge branch 'main' into main
OberonDixon
authored