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base repository: jdoughertyii/PyVCF
base: master
head repository: jamescasbon/PyVCF
compare: master
Commits on Oct 30, 2011
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James Casbon committed
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minimal setup to get into pythonpath
James Casbon committedOct 30, 2011 Configuration menu - View commit details
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vcf_melt for turning wide tsv into long tsv
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Commits on Nov 2, 2011
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convienience methods for changing a record
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Commits on Jan 12, 2012
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Merge remote-tracking branch 'upstream/master'
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add meta to setup.py, note about fork to README
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Commits on Jan 16, 2012
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Tolerate negative Number values in INFO and FORMAT fields
Negative values for the Number entry in INFO and FORMAT fields are not allowed by the VCF spec, but we see them in practice (samtools uses -1 in the PL format). We silently convert them to None or '.'.
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use ordered dict for samples, fixes #2
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remove redundant code now using ordereddict
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make ordered sample dictionary backwards compatible, add documentation
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update README.rst, add HISTORY, fix doctests
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update doctest for sample objects
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include VCFWriter class and test cases
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change vcf.VCFReader to vcf.Reader
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change vcf.VCFReader to vcf.Reader (docs)
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Commits on Jan 17, 2012
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parse meta when initing the reader, rather than at iteration
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support opening via filename and gzipped data
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Support fetching from tabix files, fixes #7
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Commits on Jan 18, 2012
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test for 1kg files, allow QUAL=.
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drop meta info decorator for performance, meta info parsed in init
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speed optimisations, drop properties for direct access
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Commits on Jan 19, 2012
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Remove ordereddict for performance, replace with genotype method for
lookup of genotypes
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Commits on Jan 20, 2012
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writer now correctly writes metadata
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initial work on an extensible VCF filter
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add filter lines, but writer needs improvement
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vcf filter now inserts into meta, applies ok
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Commits on Jan 21, 2012
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performance: stop processing a call if the genotype is ./.
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backwards compatible call data lookup
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