Change Log


Released 2018-01-15

New features

  • (#5072) Added multi-phenotype option to hl.logistic_regression_rows
  • (#5077) Added support for importing VCF floating-point FORMAT fields as float32 as well as float64.


  • (#5068) Improved optimization of MatrixTable.count_cols.
  • (#5131) Fixed performance bug related to hl.literal on large values with missingness

Bug fixes

  • (#5088) Fixed name separator in MatrixTable.make_table.
  • (#5104) Fixed optimizer bug related to experimental functionality.
  • (#5122) Fixed error constructing Table or MatrixTable objects with fields with certain character patterns like $.


Released 2019-01-03

New features

  • (#5046)(experimental) Added option to BlockMatrix.export_rectangles to export as NumPy-compatible binary.

Performance improvements

  • (#5050) Short-circuit iteration in logistic_regression_rows and poisson_regression_rows if NaNs appear.


Released 2018-12-17

New features

  • (#4962) Expanded comparison operators (==, !=, <, <=, >, >=) to support expressions of every type.
  • (#4927) Expanded functionality of Table.order_by to support ordering by arbitrary expressions, instead of just top-level fields.
  • (#4926) Expanded default GRCh38 contig recoding behavior in import_plink.

Performance improvements

  • (#4952) Resolved lingering issues related to (#4909).

Bug fixes

  • (#4941) Fixed variable scoping error in regression methods.
  • (#4857) Fixed bug in maximal_independent_set appearing when nodes were named something other than i and j.
  • (#4932) Fixed possible error in export_plink related to tolerance of writer process failure.
  • (#4920) Fixed bad error message in Table.order_by.


Released 2018-12-07

New features

  • (#4845) The or_error method in and hl.switch statements now takes a string expression rather than a string literal, allowing more informative messages for errors and assertions.
  • (#4865) We use this new or_error functionality in methods that require biallelic variants to include an offending variant in the error message.
  • (#4820) Added hl.reversed for reversing arrays and strings.
  • (#4895) Added include_strand option to the hl.liftover function.

Performance improvements

  • (#4907)(#4911) Addressed one aspect of bad scaling in enormous literal values (triggered by a list of 300,000 sample IDs) related to logging.
  • (#4909)(#4914) Fixed a check in Table/MatrixTable initialization that scaled O(n^2) with the total number of fields.

Bug fixes

  • (#4754)(#4799) Fixed optimizer assertion errors related to certain types of pipelines using group_rows_by.
  • (#4888) Fixed assertion error in BlockMatrix.sum.
  • (#4871) Fixed possible error in locally sorting nested collections.
  • (#4889) Fixed break in compatibility with extremely old MatrixTable/Table files.
  • (#4527)(#4761) Fixed optimizer assertion error sometimes encountered with hl.split_multi[_hts].

0.2.4: Beginning of history!

We didn’t start manually curating information about user-facing changes until version 0.2.4.

The full commit history is available here.