moonso/genmod — pull request #12 by tzhughes (2014-05-07 09:48:37+00:00)
Title: Testing FAM file deviations

I have set up some tests for FAM files
```
cd test_famFile
runTests.bash
```

I think these tests can be quite useful as it is in the FAM file that human error is most likely to creep in:
* an extra column causing sex or affected status to be wrongly interpreted
* missing column
* mother that is male
* individuals without relationships to each other
And this obviously has a big impact on the annotations.

Basically I have one test FAM file that should run through and all the others should raise exceptions or warnings (in my opinion), but only the `standardTrio_missingColForSon.fam` does.

Several of the tests are a bit trivial, but one that is a bit more critical is the `standardTrio_noRelationships.fam` where none of the people in the family are related to each other. This runs through and annotates the son as AR. Technically speaking this is correct because his relationship to the mother and father are gone from the FAM file, but it creates the same problem as when a sample in the VCF is not specified in the FAM file ie you get annotations in the VCF that are based on a subset of the genotypes present.

Let me know what you think.