Code

feat: iterative approach#47

Code

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aryarm merged 41 commits intofeat/ukbgymrek-lab/happler:feat/ukbfrom feat/forestsgymrek-lab/happler:feat/forestsCopy head branch name to clipboardDec 5, 2024

+1,921-509

Commits

Commits on Sep 25, 2024

• create first iteration of forest builder

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Commits on Sep 30, 2024

• use new config file for simulations

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• use new --max-signals param in happler

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• make simulate workflow reproducible

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• output multiple haps in choose_different_ld

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• try (and fail) to import graphviz trees

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• simply output an empty file when all haps are SNPs

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• enable graphviz output for multiple trees

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Commits on Oct 7, 2024

• simulate multiple haps as well

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• match obs and causal haps by their LD

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Commits on Oct 16, 2024

• implement a final haplotype threshold too

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• color each point of the parameter plot by whether it is an extra

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Commits on Oct 17, 2024

• enable simulation replicates

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Commits on Oct 22, 2024

• output finemapping metrics for multiple haps

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Commits on Oct 23, 2024

• allow for setting output threshold as a param in the config

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• clean up and update scripts README

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• handle empty hap files in utils.R

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• allow for reordering rows of parameter_plot

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• allow for leniency when estimating pvals in happler

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• make thresh more lenient

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• split pheno for happler rules

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Commits on Oct 24, 2024

• set up workflow for running on geuvadis again

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• switch to geuvadis config

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• enable pickling as a parameter plot option

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Commits on Oct 25, 2024

• start to try to handle multiple haps in summarize_results.R

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• enable computing mean and stderr of finemapping metrics in parameter_plot

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• adjust the amount of time for the multiline rule

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• start on STR analysis

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• revert to min for now. need to come up with a better way of doing this eventually

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Commits on Oct 30, 2024

• allow for pickled output for explained_variances.png

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Commits on Nov 22, 2024

• upgrade to newest susie

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• recalibrate timing and mem

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• collapse sim configs

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Commits on Nov 26, 2024

• switch to dev version of haptools

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• ci: handle deprecations in gh actions and devcontainer

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• update lock file for latest haptools

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• update min python to 3.9 and add 3.13 ci test

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• fix failing example tests with --out-thresh

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• refmt with black

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Commits on Dec 5, 2024

• adapt workflow to simulate STRs

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• update lock file

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