@Override
public ListVector convert(Iterable<Genotype> genotypes) {
NamedBuilder fullBuilder = ListVector.newNamedBuilder();
// add a named element in the build for each sample
for (Genotype gt : genotypes) {
NamedBuilder itemBuilder = ListVector.newNamedBuilder();
// add id
itemBuilder.add("ID", gt.getSampleName());
if (header == null) {
// only add genotype
itemBuilder.add("GT", getGT(gt));
} else {
itemBuilder.add("GT", getGT(gt));
Collection<VCFFormatHeaderLine> formatLines = header.getFormatHeaderLines();
for (VCFFormatHeaderLine hl : formatLines) {
String key = hl.getID();
VCFHeaderLineType type = hl.getType();
if (key.equals("GT")) {
continue;
}
Object val = gt.getAnyAttribute(key);
switch (type) {
case String:
{
if (val instanceof List<?>) {
List<String> items = (List<String>) val;
StringArrayVector vec = new StringArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof String[]) {
String[] items = (String[]) val;
StringArrayVector vec = new StringArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof String) {
String items = (String) val;
StringArrayVector vec = new StringArrayVector(items);
itemBuilder.add(key, vec);
}
break;
}
case Float:
{
if (val instanceof List<?>) {
List<Double> items = (List<Double>) val;
DoubleArrayVector vec = new DoubleArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof Double[]) {
double[] items = ArrayUtils.toPrimitive((Double[]) val);
DoubleArrayVector vec = new DoubleArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof Double) {
Double items = (Double) val;
DoubleArrayVector vec = new DoubleArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof String) {
Double items = Double.parseDouble((String) val);
DoubleArrayVector vec = new DoubleArrayVector(items);
itemBuilder.add(key, vec);
}
break;
}
case Integer:
{
if (val instanceof List<?>) {
List<Integer> items = (List<Integer>) val;
int[] arr = new int[items.size()];
for (int i = 0; i < items.size(); i++) {
arr[i] = items.get(i);
}
IntArrayVector vec = new IntArrayVector(arr);
itemBuilder.add(key, vec);
} else if (val instanceof Integer[]) {
int[] items = ArrayUtils.toPrimitive((Integer[]) val);
IntArrayVector vec = new IntArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof Integer) {
Integer items = (Integer) val;
IntArrayVector vec = new IntArrayVector(items);
itemBuilder.add(key, vec);
} else if (val instanceof String) {
Integer items = Integer.parseInt((String) val);
IntArrayVector vec = new IntArrayVector(items);
itemBuilder.add(key, vec);
}
break;
}
case Character:
{
char value = (char) gt.getAnyAttribute(key);
itemBuilder.add(key, new String(new char[] {value}));
break;
}
default:
throw new IllegalStateException(type + " is not supported");
}
}
}
fullBuilder.add(gt.getSampleName(), itemBuilder.build());
}
return fullBuilder.build();
}
