public static String prettyPrintSequenceRecords(SAMSequenceDictionary sequenceDictionary) {
String[] sequenceRecordNames = new String[sequenceDictionary.size()];
int sequenceRecordIndex = 0;
for (SAMSequenceRecord sequenceRecord : sequenceDictionary.getSequences())
sequenceRecordNames[sequenceRecordIndex++] = sequenceRecord.getSequenceName();
return Arrays.deepToString(sequenceRecordNames);
}
private static void setIndexSequenceDictionary(
final Index index, final SAMSequenceDictionary dict) {
for (final SAMSequenceRecord seq : dict.getSequences()) {
final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName();
final String length = String.valueOf(seq.getSequenceLength());
index.addProperty(contig, length);
}
}
/**
* create a list of genomic locations, given a reference sequence
*
* @param dict the sequence dictionary to create a collection from
* @return the GenomeLocSet of all references sequences as GenomeLoc's
*/
public static GenomeLocSortedSet createSetFromSequenceDictionary(SAMSequenceDictionary dict) {
GenomeLocParser parser = new GenomeLocParser(dict);
GenomeLocSortedSet returnSortedSet = new GenomeLocSortedSet(parser);
for (SAMSequenceRecord record : dict.getSequences()) {
returnSortedSet.add(
parser.createGenomeLoc(record.getSequenceName(), 1, record.getSequenceLength()));
}
return returnSortedSet;
}