Hail 0.2.10 patch notes

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0.2.10

Released 2019-02-15

New features

  • (#5272) Added a new ‘delimiter’ option to Table.export.
  • (#5251) Add utility aliases to hl.plot for output_notebook and show.
  • (#5249) Add histogram2d function to hl.plot module.
  • (#5247) Expose MatrixTable.localize_entries method for converting to a Table with an entries array.
  • (#5300) Add new filter and find_replace arguments to hl.import_table and hl.import_vcf to apply regex and substitutions to text input.

Performance improvements

  • (#5298) Reduce size of exported VCF files by exporting missing genotypes without trailing fields.

Bug fixes

  • (#5306) Fix ReferenceGenome.add_sequence causing a crash.
  • (#5268) Fix Table.export writing a file called ‘None’ in the current directory.
  • (#5265) Fix hl.get_reference raising an exception when called before hl.init().
  • (#5250) Fix crash in pc_relate when called on a MatrixTable field other than ‘GT’.
  • (#5278) Fix crash in Table.order_by when sorting by fields whose names are not valid Python identifiers.
  • (#5294) Fix crash in hl.trio_matrix when sample IDs are missing.
  • (#5295) Fix crash in Table.index related to key field incompatibilities.

0.2.9

Released 2019-01-30

New features

  • (#5149) Added bitwise transformation functions: hl.bit_{and, or, xor, not, lshift, rshift}.
  • (#5154) Added hl.rbind function, which is similar to hl.bind but expects a function as the last argument instead of the first.

Performance improvements

  • (#5107) Hail’s Python interface generates tighter intermediate code, which should result in moderate performance improvements in many pipelines.
  • (#5172) Fix unintentional performance deoptimization related to Table.show introduced in 0.2.8.
  • (#5078) Improve performance of hl.ld_prune by up to 30x.

Bug fixes

  • (#5144) Fix crash caused by hl.index_bgen (since 0.2.7)
  • (#5177) Fix bug causing Table.repartition(n, shuffle=True) to fail to increase partitioning for unkeyed tables.
  • (#5173) Fix bug causing Table.show to throw an error when the table is empty (since 0.2.8).
  • (#5210) Fix bug causing Table.show to always print types, regardless of types argument (since 0.2.8).
  • (#5211) Fix bug causing MatrixTable.make_table to unintentionally discard non-key row fields (since 0.2.8).

0.2.8

Released 2019-01-15

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.

Performance improvements

  • (#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 $.

0.2.7

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.