innovativemedicine/vcfimp — pull request #4 by adamnovak (2014-01-15 18:39:07+00:00)
Title: Improved compliance with VCF spec, bumped version to 0.6.1

I have fixed several bugs with regard to the implementation of the VCF spec as described at:
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

The vcfimp library can now parse the example VCF file given on that page.

Specifically, I have improved support for the missing value "." notation in the VCF spec, adding a new VcfMissing type to represent it, and allowing it in a number of places where the spec allowed it but the parser did not.

I have also disentangled the namespaces for different kinds of metadata; the spec allows you to have say, an INFO named "GT" and a FORMAT named "GT" in the same file, while the parser formerly did not.

All of the parser fixes have associated test cases that the old parser failed but the new parser passes.

Because I have made bugfix changes to the behavior of the parser, I have bumped the version number to 0.6.1 from 0.6.0, so that the version with the changes can be required as a dependency.