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Development

Please use the PyVCF repository. Pull requests gladly accepted. Issues should be reported at the github issue tracker.

Running tests

Please check the tests by running them with:

python setup.py test

New features should have test code sent with them.

Changes

0.6.7 Release

  • Include missing .pyx files

0.6.6 Release

  • better walk together record ordering (Thanks @datagram, #141)

0.6.5 Release

  • Better contig handling (#115, #116, #119 thanks Martijn)
  • INFO lines with type character (#120, #121 thanks @AndrewUzilov, Martijn)
  • Single breakends fix (#126 thanks @pkrushe)
  • Speedup by losing ordering of INFO (#128 thanks Martijn)
  • HOMSEQ and other missing fields in INFO (#130 thanks Martijn)
  • Add aaf property, (thanks @mgymrek #131)
  • Custom equality for walk_together, thanks bow #132
  • Change default line encoding to 'n'
  • Improved __eq__ (#134, thanks bow)

0.6.4 Release

  • Handle INFO fields with multiple values, thanks
  • Support writing records without GT data #88, thanks @bow
  • Pickleable call data #112, thanks @superbobry
  • Write files without FORMAT #95 thanks Martijn
  • Strict whitespace mode, thanks Martijn, Lee Lichtenstein and Manawsi Gupta
  • Add support for contigs in header, thanks @gcnh and Martijn
  • Fix GATK header parsing, thanks @alimanfoo

0.6.3 Release

  • cython port of #79
  • correct writing of meta lines #84

0.6.2 Release

  • issues #78, #79 (thanks Sean, Brad)

0.6.1 Release

  • Add strict whitespace mode for well formed VCFs with spaces in sample names (thanks Marco)
  • Ignore blank lines in files (thanks Martijn)
  • Tweaks for handling missing data (thanks Sean)
  • bcftools tests (thanks Martijn)
  • record.FILTER is always a list

0.6.0 Release

  • Backwards incompatible change: _Call.data is now a namedtuple (previously it was a dict)
  • Optional cython version, much improved performance.
  • Improvements to writer (thanks @cmclean)
  • Improvements to inheritance of classes (thanks @lennax)

0.5.0 Release

  • VCF 4.1 support: - support missing genotype #28 (thanks @martijnvermaat) - parseALT for svs #42, #48 (thanks @dzerbino)
  • trim_common_suffix method #22 (thanks @martijnvermaat)
  • Multiple metadata with the same key is stored (#52)
  • Writer improvements: - A/G in Number INFO fields #53 (thanks @lennax) - Better output #55 (thanks @cmclean)
  • Allow malformed INFO fields #49 (thanks @ilyaminkin)
  • Added bayes factor error bias VCF filter
  • Added docs on vcf_melt
  • filters from @libor-m (SNP only, depth per sample, avg depth per sample)
  • change to the filter API, use docstring for filter description

0.4.6 Release

  • Performance improvements (#47)
  • Preserve order of INFO column (#46)

0.4.5 Release

  • Support exponent syntax qual values (#43, #44) (thanks @martijnvermaat)
  • Preserve order of header lines (#45)

0.4.4 Release

  • Support whitespace in sample names
  • SV work (thanks @arq5x)
  • Python 3 support via 2to3 (thanks @marcelm)
  • Improved filtering script, capable of importing local files

0.4.3 Release

  • Single floats in Reader._sample_parser not being converted to float #35
  • Handle String INFO values when Number=1 in header #34

0.4.2 Release

  • Installation problems

0.4.1 Release

  • Installation problems

0.4.0 Release

  • Package structure
  • add vcf.utils module with walk_together method
  • samtools tests
  • support Freebayes' non standard '.' for no call
  • fix vcf_melt
  • support monomorphic sites, add is_monomorphic method, handle null QUALs
  • filter support for files with monomorphic calls
  • Values declared as single are no-longer returned in lists
  • several performance improvements

0.3.0 Release

  • Fix setup.py for python < 2.7
  • Add __eq__ to _Record and _Call
  • Add is_het and is_variant to _Call
  • Drop aggressive parse mode: we're always aggressive.
  • Add tabix fetch for single calls, fix one->zero based indexing
  • add prepend_chr mode for Reader to add chr to CHROM attributes

0.2.2 Release

Documentation release

0.2.1 Release

  • Add shebang to vcf_filter.py

0.2 Release

  • Replace genotype dictionary with a Call object
  • Methods on Record and Call (thanks @arq5x)
  • Shortcut parse_sample when genotype is None

0.1 Release

  • Added test code
  • Added Writer class
  • Allow negative number in INFO and FORMAT fields (thanks @martijnvermaat)
  • Prefer vcf.Reader to vcf.VCFReader
  • Support compressed files with guessing where filename is available on fsock
  • Allow opening by filename as well as filesocket
  • Support fetching rows for tabixed indexed files
  • Performance improvements (see test/prof.py)
  • Added extensible filter script (see FILTERS.md), vcf_filter.py

Contributions

Project started by @jdoughertyii and taken over by @jamescasbon on 12th January 2011. Contributions from @arq5x, @brentp, @martijnvermaat, @ian1roberts, @marcelm.

This project was supported by Population Genetics.

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