/**
* Parse one sample file and integrate it with samples that are already there Fail quickly if we
* find any errors in the file
*/
private Collection<Sample> addSamplesFromPedigreeArgument(File sampleFile) {
final PedReader reader = new PedReader();
try {
return reader.parse(sampleFile, getMissingFields(sampleFile), sampleDB);
} catch (FileNotFoundException e) {
throw new UserException.CouldNotReadInputFile(sampleFile, e);
}
}
private Collection<Sample> addSamplesFromPedigreeArgument(final String string) {
final PedReader reader = new PedReader();
return reader.parse(string, getMissingFields(string), sampleDB);
}