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CHANGELOG.md

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BioMed Sheets Changelog

0.11.7 (2023-02-22)

Bug Fixes

  • MANIFEST.in file for CHANGELOG.md (#32) (c093555)

0.11.6 (2023-02-22)

Bug Fixes

v0.11.5

  • Fixing consistency check for Duo Cases (#26).

v0.11.4

  • Fixing issues with ResourceAdapter (#21).

v0.11.3

  • Fixing warnings in the tests (#19).

v0.11.2

  • Updating/modernizing dependencies.

v0.11.1

  • Adding property to shortcut sheets that indicates available kwargs.

v0.11.0

  • Adding custom option to join pedigrees by fields such as familyId.

v0.10.0

  • Adding functionality for filtering pedigrees.

v0.9.1

  • Fixing sorting bug.

v0.9.0

  • Sorting donors for picking the index in germline sample sheets.

v0.8.1

  • Fixing mapping of Unknown values.

v0.8.0

  • Changed behaviour in case of no affected donor has library. In this case, the first donor becomes the index. Consequently, the index must have an NGS library.

v0.7.1

  • Removing superflous print.

v0.7.0

  • Allowing to specify bioSample and testSample in germline TSV files.
  • Fixing some tests.

v0.6.2

  • Proper merging with recent ruamel.yaml updates.

v0.6.1

  • Interpreting # in TSV files in more locations.

v0.6.0

  • Allowing to comment out lines in TSV files by prefixing them with #.

v0.5.6

  • Fixing bug in computing index (for real).

v0.5.5

  • Fixing bug in computing index.

v0.5.4

  • Fixing setup.py to work with pip v10.t

v0.5.3

  • Fixing packaging to use base and not test dependencies.

v0.5.2

  • Removing some hard (transitive) dependencies.

v0.5.1

  • Fixing manifest so the package contains the JSON file.

v0.5

  • Allow cancer sheets for use in germline calling.
  • Only warn if index has no NGS library, no error.

v0.4

  • Fixin TSV I/O.
  • Bumping ruamel.yaml version.
  • Fixing cancer sheet iteration.
  • Allowing cancer-only samples in cance case sheets.
  • Fixing float-related bug.
  • Fixing bug in reference resolving (+tests)

v0.3.1

  • Fixing setup.py to work with pip v10.

v0.3

  • Adding possibility for generic TSV sample sheets.
  • Many updates to make documentation more clear.
  • Various updates, fixing Codacy issues.
  • Adding routines for writing out PED file from germline sample sheets.

v0.2

  • Auto-deployment to pypi
  • Fixing shortcuts to father/mother during cohort loading
  • Cleanup code (according to Flake 8)
  • Adding more tests, replacing examples by TSV files
  • Removing protein pools
  • Adding Sphinx-based ocumentation
  • Restructuring requirements txt files
  • Configurable entity name generation. This allows to use secondary id only for naming, e.g.
  • Fixing requirements*.txt files for always using SSH
  • Fixing sample naming for germline sample sheets
  • Adding versioneer integration

v0.1.1

  • First actual release, versioning done using versioneer
  • Everything is new!