This thread documents breaking changes as we work toward stabilizing the development branch (i.e., master, 0.2 beta) as Hail 0.2 proper.

Removed as_array parameter from PCA pca and hwe_normalized_pca no longer take an as_array parameter. They now always return scores and loadings as arrays (formerly the as_array=True option). See the overview tutorial for example usage in GWAS, where PC1 becomes scores[0]. https://github.com/hail-…

Removed dataset parameter from eight methods All methods that took a dataset and at least one required expression on that dataset no longer take a dataset parameter at all (the dataset is implicitly the source of the expression): grm linear_regression logistic_regression linear_mixed_regression …

Changed ys to y and schema in linear regression Consistent with the other statistics methods, the parameter ys on linear_regression is now y, and when y is an expression the linreg fields all have type float64. This is consistent with the other regression methods. When y is a list of expressions (…

See: [image] [Breaking change] New changes to select, annotate, key_by interface for 0.2 Updates https://github.com/hail-is/hail/pull/3297 This PR will change the way keys on Tables and MatrixTables are dealt with in certain functions. (The doc links will be updated once …

Oops. See: [image] [Breaking change] Filter alleles Updates Though we have reason to believe nobody has been using this method, we are committed to announcing all breaking changes! The interface for filter_alleles has changed. Take a look at the new methods: hl.filter_al…

ld_prune has changed to take a CallExpression instead of a matrix table. The new signature is ld_prune(call_expr, r2=0.2, window=1000000, memory_per_core=256). See: https://github.com/hail-is/hail/pull/3518

ld_prune no longer requires unphased genotypes (though it still makes no use of phasing information). And the parameter window has been renamed bp_window_size. See: https://github.com/hail-is/hail/pull/3575

While we’re at it, it also returns a Table with just ('locus', 'alleles') that is the set of independent variants at that threshold (rather than previously returning the MatrixTable filtered to that set).

See: [image] [Breaking change] Hail 0.2 no longer supports BGEN 1.1 Updates As of the PR support only bgen12 , Hail 0.2 no longer supports BGEN 1.1 and only supports BGEN 1.2 with the 8-bit genotype probability encoding. If you have BGEN 1.1 data (or 1.2 with non-8-bit en…

see: [image] [Breaking Change] Hail 0.2 import_bgen should be passed a min_partitions parameter Updates Previously, some Spark heuristics chose a reasonable number of partitions for import_bgen. This logic has been removed while we improve bgen performance (we may add the …

Log of breaking changes in 0.2 beta

Updates

jbloom July 31, 2018, 1:09pm 13

see:

Topic		Replies	Views
Announcing Hail 0.2! Updates	0	4953	October 18, 2018
Hail 0.2 - Changes to data structure in the newest version? Pipeline broken in multiple places Hail Query & hailctl	4	929	May 6, 2018
[Breaking Change] Hail 0.2 removed KinshipMatrix, linear_mixed_regression Updates	17	1488	October 24, 2018
Results from linear regression are array instead of float Hail Query & hailctl	3	442	October 29, 2021
[BREAKING CHANGE] redesign of regression (GWAS) functions Updates	1	722	October 16, 2018

Log of breaking changes in 0.2 beta

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