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master: 88%

Ran 22 Apr 2016 08:35PM UTC

Files 21

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Committed 22 Apr 2016 07:57PM UTC coverage: 86.811%. First build

Job # 93.2

Build Type

push

travis-ci

Committed by

timodonnell

Commit Message

Parse sample info, including support for multisample VCFs

Add per-sample info to vcf loading. Works the same whether you use `load_vcf`
or `load_vcf_fast`.

The VariantCollection.metadata entry for each variant now includes a
`sample_info` entry, which maps samples names to a dict of pyvcf-parsed
per-sample attributes for that sample.

I think this takes care of the "support multisample vcf" issues. Summary is:

 * a `VariantCollection` is multisample: it contains whatever variants were in your VCF
 * the `VariantCollection.metadata` dict includes per-sample info (as well as across-sample info from the INFO column and filters, etc.)
 * if you care about what sample a variant was "called" in, it is left to the user to look at the genotype and decide what to do. For most VCFs this will be available in `VariantCollection.metadata[variant]['sample_info']['GT']` and the value '0/0' means no-call and anything else means there was a call. We don't assume anything about this field here though (similarly to pyvcf).

Run Details

1119 of 1289 relevant lines covered (86.81%)

0.87 hits per line

hammerlab / varcode / 93 / 2
87%
master: 88%

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