Code

feat: finish running on geuvadis#43

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aryarm merged 131 commits intomaingymrek-lab/happler:mainfrom feat/multiple-testinggymrek-lab/happler:feat/multiple-testingCopy head branch name to clipboardJun 5, 2024

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Commits

Commits on Sep 17, 2023

• wip: classes for multiple multiple-testing corrections

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Commits on Sep 26, 2023

• integrate corrections into Terminator

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Commits on Oct 1, 2023

• fix issues with corrector class

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Commits on Oct 2, 2023

• try to generate simple plot with different alpha values

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Commits on Nov 13, 2023

• standardize in validate_linreg_methods

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• disable multiple testing corrections by default

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  a72b7f2

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• subset gt file by samples in pt file first

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  f846daa

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• add happler transform command

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• also show direction of LD in plots

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• allow for comparing LD between causal and observed haps

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• prune the negative allele but keep the positive one

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Commits on Nov 14, 2023

• handle single gwas in manhattan script

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Commits on Nov 21, 2023

• make manhattan script more modular

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Commits on Nov 28, 2023

• remove multiple testing corrections as we add more nodes to a branch

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  1770ca3

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Commits on Dec 5, 2023

• fix broken code in summarize_results.R

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  d2d0ac2

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• revise broken code from refactor

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Commits on Dec 12, 2023

• make ld_range potentially reproducible

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• switch from runtime to runtime_min

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Commits on Dec 13, 2023

• try adding support for random haps

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  815d001

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• fix miscellaneous errors

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  5ca12d2

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• allow for arbitrary haplotype IDs hap files

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  d6cb28d

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• move causal_gt param to inputs

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• handle case where causal hap is also within input

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Commits on Dec 15, 2023

• handle case with no hap

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Commits on Dec 21, 2023

• add susie metrics script

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• add bash script for running on tscc 2.0

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Commits on Jan 4, 2024

• add cluster-sync command

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• add step to plot finemapping metrics

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Commits on Jan 18, 2024

• create simpler version of haptools ld command

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Commits on Jan 28, 2024

• reinstate hap mode support

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Commits on Feb 2, 2024

• modify run.bash to run on slurm

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• allow for specifying various sample sizes

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Commits on Feb 8, 2024

• start on geuvadis workflow

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• install peer script in default env

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• add Michael's peer residual script

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Commits on Feb 9, 2024

• try to use region param in entire happler workflow

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Commits on Feb 10, 2024

• use maf in happler script

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• create separate env with peer since it conflicts

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Commits on Feb 11, 2024

• run happler pipeline until gwas but not manhattan

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  4a6a40e

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• support inferring orange hap ids in manhattan plot

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  ecfd1d5

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• implement region pgen handling code in R scripts

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Commits on Feb 20, 2024

• remove double log file

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  f008959

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• give up on running covariates and just use residuals instead

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• run 1000G different sample sizes

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Commits on Feb 21, 2024

• enable plotting module to handle sampsize and locus wildcards

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Commits on Mar 12, 2024

• run on geuvadis

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Commits on Mar 21, 2024

• ensure scientific notat not used and liftover regions

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Commits on Mar 28, 2024

• compute pgen ld a little faster

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• also enable computing allele LD heatmaps

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• fix happler_results rule when in 'run' mode

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Commits on Mar 31, 2024

• enable debug mode via config

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• plot finemapping without causal variable

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Commits on Apr 1, 2024

• add r debugging function

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• allow summarize_results.R to work wo causal variant

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• fix issue with loading pgen data in R with region

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Commits on Apr 2, 2024

• add SVs to manhattan plots

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• switch to snakemake 8 and slurm executor

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Commits on Apr 4, 2024

• add table at bottom of allele heatmap

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• switch to black and white

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Commits on Apr 8, 2024

• convert white to gray in LD heatmap

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Commits on Apr 9, 2024

• make script for plotting pts vs gts for a hap

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• add boxplots to normal snakemake output

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Commits on Apr 12, 2024

• try to batch igv

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Commits on Apr 16, 2024

• add IGV plotting

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• update to snakemake8

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Commits on Apr 18, 2024

• add plot for variance explained

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• refactor variance_explained and remove linears param

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Commits on Apr 19, 2024

• allow for extracting PIPs to a TSV

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• update to latest haptools

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• use inplace subset of phenotypes

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Commits on Apr 22, 2024

• upgradesnakemake version

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• create conditional linreg plots

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Commits on Apr 26, 2024

• add original manhattan to conditional regression plot

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• revise run.bash to work with condo instead of hotel

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Commits on Apr 30, 2024

• use set instead of tuple of samples after updating haptools

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• use only a specific hap in the IGV plots

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  2f9fb61

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• try the strict branching strategy instead

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Commits on May 1, 2024

• create script for computing residuals

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• add residual computation and split_pheno scripts

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  c226788

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• fix comment in residuals script

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Commits on May 4, 2024

• handle samples that are phenotyped but not genotyped

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Commits on May 6, 2024

• use 'trait' instead of 'gene' as wildcard name

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• tweak workflow slightly for running on UKB

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Commits on May 7, 2024

• upgrade plink2 in workflow

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• do not import simulation workflow if just running happler

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• ensure withdrawn samples are removed not kept

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• make ukb config the default instead

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• add space after param in genotypes module

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  7a6a3d6

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• fix issue where we were only running one locus for each trait

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Commits on May 13, 2024

• prune even with the strict branching strategy

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Commits on May 21, 2024

• fix broken workflow after removing --no-temp

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Commits on May 22, 2024

• fix labeling of manhattans

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Commits on May 24, 2024

• handle buffer/padding in heatmap plots

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• switch from shapeit to beagle bc it's faster

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Commits on May 28, 2024

• ensure chosen haplotypes exceed maf threshold

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Commits on May 30, 2024

• add test for 1000G test dataset

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• disable filtering with maf of None

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  f7296ea

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• fix bug in maf masking and add proper test

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• switch to symlink for config file

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  f3cc6b1

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• upgrade to latest snakemake

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• try to use less memory while tree building

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Commits on May 31, 2024

• add checkpoint to check which loci have multi-variant haps

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• provide best allele idx instead of best res idx

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  636652a

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• fix bugs in multiline checkpoint

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  f4731a9

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• update to latest beagle and reduce happler runtime

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• add extra plots to output

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• filter by maf in all happler steps

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Commits on Jun 2, 2024

• add test with real data

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• fix error when output is stdout but --show-tree is given

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• fix bug when terminating strict branching with an maf threshold

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Commits on Jun 3, 2024

• try to switch to dev-env.yml file

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• update pyproject to use only py3.8+

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• remove py3.7 from ci

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• update sphinx-autodoc-typehints

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• add statsmodels and update sphinx-autodoc-typehints again

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• disable macos ci for now

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• also add SV analysis to target rule

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• try to use custom formula for memory requirement

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• use custom formula for runtime as well

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Commits on Jun 4, 2024

• fix rtd issue

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• refmt with black

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  2aa71bb

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• re-adjust memory to work for more cases

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• Merge branch 'feat/multiple-testing' of github.com:gymrek-lab/happler into feat/multiple-testing

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• fix bool typing rtd err

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  346a442

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• fix remaining rtd issues again

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• try to resolve issues with newer versions of packages

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• lower maf thresh and try to rerun happler

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Commits on Jun 5, 2024

• skip debug log for real example and only log tree when needed

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• refmt with black

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  0c5399a

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• try to fix last rtd warning

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• increase time for vcf2plink command

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