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Changelog

0.13.8 (2024-01-10)

Bug Fixes

0.13.7 (2024-01-10)

Bug Fixes

  • remove versioneer Python 3.12 compatibility (#160) (5e2860e)

0.13.6 (2022-11-28)

  • Fixing bug in setup.py that prevented pysam dependency to be loaded (#150).

v0.13.5 (2022-11-13)

  • Treat .bgz files the same as .gz (#145, #149)

v0.13.4 (2022-04-13)

  • Switching to Github Actions for CI
  • Fix INFO flag raises TypeError (#146)

v0.13.3 (2020-09-14)

  • Adding Record.update_calls.
  • Making Record.{format,calls} use list when empty

v0.13.2 (2020-08-20)

  • Adding Call.set_genotype().

v0.13.1 (2020-08-20)

  • Fixed Call.ploidy.
  • Fixed Call.is_variant.

v0.13.0 (2020-07-10)

  • Fixing bug in case GT describes only one allele.
  • Proper escaping of colon and semicolon (or the lack of escaping) in INFO and FORMAT.

v0.12.2 (2020-04-29)

  • Fixing bug in case GT describes only one allele.

v0.12.1 (2019-03-08)

  • Not warning on PASS filter if not defined in header.

v0.12.0 (2019-01-29)

  • Fixing tests for Python >=3.6
  • Fixing CI, improving tox integration.
  • Applying black formatting.
  • Replacing Makefile with more minimal one.
  • Removing some linting errors from flake8.
  • Adding support for reading VCF without FORMAT or any sample column.
  • Adding support for writing headers and records without FORMAT and any sample columns.

v0.11.2 (2018-04-16)

  • Removing pip module from setup.py which is not recommended anyway.

v0.11.1 (2018-03-06)

  • Working around problem in HTSJDK output with incomplete FORMAT fields (#127). Writing out . instead of keeping trailing empty records empty.

v0.11.0 (2017-11-22)

  • The field FORMAT/FT is now expected to be a semicolon-separated string. Internally, we will handle it as a list.
  • Switching from warning helper utility code to Python warnings module.
  • Return str in case of problems with parsing value.

v0.10.0 (2017-02-27)

  • Extending API to allow for reading subsets of records. (Writing for sample subsets or reordered samples is possible through using the appropriate names list in the SamplesInfos for the Writer).
  • Deep-copying header lines and samples infos on Writer construction
  • Using samples attribute from Header in Reader and Writer instead of passing explicitely

0.9.0 (2017-02-26)

  • Restructuring of requirements.txt files
  • Fixing parsing of no-call GT fields

0.8.1 (2017-02-08)

  • PEP8 style adjustments
  • Using versioneer for versioning
  • Using requirements*.txt files now from setup.py
  • Fixing dependency on cyordereddict to be for Python <3.6 instead of <3.5
  • Jumping by samtools coordinate string now also allowed

0.8.0 (2016-10-31)

  • Adding Header.has_header_line for querying existence of header line
  • Header.add_*_line return a bool no indicating any conflicts
  • Construction of Writer uses samples within header and no extra parameter (breaks API)

0.7.0 (2016-09-25)

  • Smaller improvements and fixes to documentation
  • Adding Codacy coverage and static code analysis results to README
  • Various smaller code cleanup triggered by Codacy results
  • Adding __eq__, __neq__ and __hash__ to data types (where applicable)

0.6.0 (2016-09-25

  • Refining implementation for breakend and symbolic allele class
  • Removing record.SV_CODES
  • Refactoring parser module a bit to make the code cleaner
  • Fixing small typos and problems in documentation

0.5.0 (2016-09-24)

  • Deactivating warnings on record parsing by default because of performance
  • Adding validation for INFO and FORMAT fields on reading (#8)
  • Adding predefined INFO and FORMAT fields to pyvcf.header (#32)

0.4.1 (2016-09-22)

  • Initially enabling codeclimate

0.4.0 (2016-09-22)

  • Exporting constants for encoding variant types
  • Exporting genotype constants HOM_REF, HOM_ALT, HET
  • Implementing Call.is_phased, Call.is_het, Call.is_variant, Call.is_phased, Call.is_hom_ref, Call.is_hom_alt
  • Removing Call.phased (breaks API, next release is 0.4.0)
  • Adding tests, fixing bugs for methods of Call

0.3.1 (2016-09-21)

  • Work around FORMAT/FT being a string; this is done so in the Delly output

0.3.0 (2016-09-21)

  • Reader and Writer can now be used as context manager (with with)
  • Including license in documentation, including Biopython license
  • Adding support for writing bgzf files (taken from Biopython)
  • Adding support for parsing arrays in header lines
  • Removing example-4.1-bnd.vcf example file because v4.1 tumor derival lacks ID field
  • Adding AltAlleleHeaderLine, MetaHeaderLine, PedigreeHeaderLine, and SampleHeaderLine
  • Renaming SimpleHeaderFile to SimpleHeaderLine
  • Warn on missing FILTER entries on parsing
  • Reordered parameters in from_stream and from_file (#18)
  • Renamed from_file to from_stream (#18)
  • Renamed Reader.jump_to to Reader.fetch
  • Adding header_without_lines function
  • Generally extending API to make it esier to use
  • Upgrading dependencies, enabling pyup-bot
  • Greatly extending documentation

0.2.1 (2016-09-19)

  • First release on PyPI