public static Map<String, VCFHeader> getVCFHeadersFromRodPrefix(
GenomeAnalysisEngine toolkit, String prefix) {
Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
// iterate to get all of the sample names
List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
for (ReferenceOrderedDataSource source : dataSources) {
// ignore the rod if lacks the prefix
if (!source.getName().startsWith(prefix)) continue;
if (source.getHeader() != null && source.getHeader() instanceof VCFHeader)
data.put(source.getName(), (VCFHeader) source.getHeader());
}
return data;
}
public static Map<String, VCFHeader> getVCFHeadersFromRods(
GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
// iterate to get all of the sample names
List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
for (ReferenceOrderedDataSource source : dataSources) {
// ignore the rod if it's not in our list
if (rodNames != null && !rodNames.contains(source.getName())) continue;
if (source.getHeader() != null && source.getHeader() instanceof VCFHeader)
data.put(source.getName(), (VCFHeader) source.getHeader());
}
return data;
}
/**
* Gets the header fields from all VCF rods input by the user
*
* @param toolkit GATK engine
* @param rodNames names of rods to use, or null if we should use all possible ones
* @return a set of all fields
*/
public static Set<VCFHeaderLine> getHeaderFields(
GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
// keep a map of sample name to occurrences encountered
TreeSet<VCFHeaderLine> fields = new TreeSet<VCFHeaderLine>();
// iterate to get all of the sample names
List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
for (ReferenceOrderedDataSource source : dataSources) {
// ignore the rod if it's not in our list
if (rodNames != null && !rodNames.contains(source.getName())) continue;
if (source.getRecordType().equals(VariantContext.class)) {
VCFHeader header = (VCFHeader) source.getHeader();
if (header != null) fields.addAll(header.getMetaDataInSortedOrder());
}
}
return fields;
}