/**
* Provides the next record from the underlying iterator after applying filter strings generated
* by the set of filters in use by the iterator.
*/
@Override
public VariantContext next() {
final VariantContext ctx = this.iterator.next();
final Set<String> filterStrings = new HashSet<String>();
// Collect variant level filters
for (final VariantFilter filter : this.filters) {
final String val = filter.filter(ctx);
if (val != null) filterStrings.add(val);
}
// Collect genotype level filters in a Map of Sample -> List<filter string>
final ListMap<String, String> gtFilterStrings = new ListMap<String, String>();
final Set<String> variantSamples = new HashSet<String>();
for (final Genotype gt : ctx.getGenotypes()) {
if (gt.isCalled() && !gt.isHomRef()) variantSamples.add(gt.getSampleName());
for (final GenotypeFilter filter : gtFilters) {
final String filterString = filter.filter(ctx, gt);
if (filterString != null) gtFilterStrings.add(gt.getSampleName(), filterString);
}
}
// If all genotypes are filtered apply a site level filter
if (gtFilterStrings.keySet().containsAll(variantSamples)) {
filterStrings.add(ALL_GTS_FILTERED);
}
// Make a builder and set the site level filter appropriately
final VariantContextBuilder builder = new VariantContextBuilder(ctx);
if (filterStrings.isEmpty()) {
builder.passFilters();
} else {
builder.filters(filterStrings);
}
// Apply filters to the necessary genotypes
builder.noGenotypes();
final List<Genotype> newGenotypes = new ArrayList<Genotype>(ctx.getNSamples());
for (final Genotype gt : ctx.getGenotypes()) {
final GenotypeBuilder gtBuilder = new GenotypeBuilder(gt);
final List<String> filtersLocal = gtFilterStrings.get(gt.getSampleName());
if (filtersLocal == null || filtersLocal.isEmpty()) {
gtBuilder.filter(PASS_FILTER);
} else {
gtBuilder.filters(filtersLocal);
}
newGenotypes.add(gtBuilder.make());
}
builder.genotypes(newGenotypes);
return builder.make();
}
@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();
}
