v0.11.0

Update deps (#208)

* try pupdate deps

* temporarily point to BGEN commit

* update CI actions

* try 1.11 in Docker

* add missing p_value_or_nan method

* make transitions be based on allele frequency instead of genotypes

* Extra treatment covariates (#207)

* add get_covariates function and use in estimands_from_groups setting with an extra treatment

* add TREAT_1 as a covariate

* update test to accomodate new functionality

* remove deprecated cached action

* remove deprecated julia action

* address Olivier's comments

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Co-authored-by: roskamsh <[email protected]>

* fix genotypes candidate not in dataset

* add some comments and doctrings

* fix missing genotypes in dataset after merge

* update dependencies

---------

Co-authored-by: roskamsh <[email protected]>

v0.10.1

Create empty QQ plot when there are not a sufficient number of p-values to generate this.

v0.10.0

• Add a make-outputs command
• Add a svp command

v0.9.0

[BREAKING]

• GWAS inputs
• single entry point
• dropped old negative control
• drop actors mode

v0.8.1

• Add support for ComposedEstimand in from_param_file mode

v0.8.0

• Add flat config [BREAKING]

v0.7.0

• Adapt TMLE and TargetedEstimation deps
• Integrate NegativeControl

v0.6.3

Deprecate the selection of :CHR column which is unused.

v0.6.2

Added new functionality to from_actors mode:

• Now compatible with multiple TFs being specified in a new column, 'TF', in the bqtls and trans_actors CSV files
• This will combine each bQTL-trans_actor on a TF-specific basis
• Original behaviour of bqtls and trans_actors CSV files not containing TF column is unchanged

v0.6.1

Make ld-block and qc files optional.