arq5x/cyvcf — pull request #2 by chapmanb (2012-07-06 12:02:44+00:00)
Title: Parse VCF with haploid calls, all no-call variants and incorrect header information

Aaron;
These are the complementary fixes for the Gemini pull request, handling:

- VCF files with haploid calls.
- Samples with all no-calls, which occur after subsetting larger files.
- Incorrectly specified header variable types. Some values specified as integers in the header actually contained floats, causing parsing to fail. This falls back to a float if integer conversion fails.

I also added a few fixes for the test suite when checking to be sure these didn't break anything. I don't believe the test changes are related to my fixes, but rather just some bits that have gotten out of date. The `walk_together` test is still failing, but I wasn't positive about the right fix so left it.