@Override
protected void setup(Context context) throws IOException, InterruptedException {
super.setup(context);
setupGCBins(context.getConfiguration());
genomeAdmin = HBaseGenomeAdmin.getHBaseGenomeAdmin(context.getConfiguration());
variationAdmin = VariationAdmin.getInstance(context.getConfiguration());
genomeName = context.getConfiguration().get("genome");
parentGenome = context.getConfiguration().get("parent");
genome = genomeAdmin.getGenomeTable().getGenome(genomeName);
if (genome == null) throw new IOException("Genome " + genome + " is missing.");
try {
SNVProbability table =
(SNVProbability) variationAdmin.getTable(VariationTables.SNVP.getTableName());
snvProbabilities = table.getProbabilities();
SizeProbability sizeTable =
(SizeProbability) variationAdmin.getTable(VariationTables.SIZE.getTableName());
sizeProbabilities = sizeTable.getProbabilities();
variationList = sizeTable.getVariationList();
variationList.add("SNV");
} catch (ProbabilityException e) {
throw new InterruptedException("Failed to start mapper: " + e);
}
varTable = (VariationCountPerBin) variationAdmin.getTable(VariationTables.VPB.getTableName());
}
@Override
public void setup(Context context) {
try {
super.setup(context);
} catch (IOException e) {
e.printStackTrace();
} catch (InterruptedException e) {
e.printStackTrace();
}
}