add PED file support

[pnrobinson]

Two options -- hard filter (remove variants that do not cosgegregate as in PhenIX) -- make this a LR test. If the variant is disease related its probability is 1, and if not, it is the probability it would have cosegregated by chance, roughly similar to a lod score. Probaby the first option is sufficient for now

[pnrobinson]

(from Jules) The Exomiser API is very simple:

Pedigree probandOnly = Pedigree justProband(String id);
Pedigree fromFile = PedFiles.readPedigree(pedPath);

And you can validate it against a VCF like this:

String probandSampleName = “proband”;
Pedigree pedigree = PedFiles.readPedigree(pedPath);
VCFHeader vcfHeader = VcfFiles.readVcfHeader(vcfPath);
List<String> sampleNames = vcfHeader.getGenotypeSamples();
SampleIdentifier probandSample = SampleIdentifierUtil.createProbandIdentifier(probandSampleName, sampleNames);
 Pedigree validatedPedigree = PedigreeSampleValidator.validate(pedigree, probandSample, sampleNames);

The InheritanceModeAnnotator uses the Jannovar API to do the analysis.