@Test
public void addRegionsOutOfOrder() {
final String contigTwoName = header.getSequenceDictionary().getSequence(2).getSequenceName();
assertTrue(mSortedSet.size() == 0);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigTwoName, 1, 50);
mSortedSet.add(g);
GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
mSortedSet.addRegion(f);
assertTrue(mSortedSet.size() == 2);
assertTrue(mSortedSet.toList().get(0).getContig().equals(contigOneName));
assertTrue(mSortedSet.toList().get(1).getContig().equals(contigTwoName));
}
protected ReadDestination(final SAMFileHeader header, final String readGroupID) {
// prepare the bam header
if (header == null) throw new IllegalArgumentException("header cannot be null");
bamHeader = new SAMFileHeader();
bamHeader.setSequenceDictionary(header.getSequenceDictionary());
bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
// include the original read groups plus a new artificial one for the haplotypes
final List<SAMReadGroupRecord> readGroups =
new ArrayList<SAMReadGroupRecord>(header.getReadGroups());
final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupID);
rg.setSample("HC");
rg.setSequencingCenter("BI");
readGroups.add(rg);
bamHeader.setReadGroups(readGroups);
}
@BeforeClass
public void beforeClass() {
header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}
@BeforeClass
public void setup() {
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
contigOneName = header.getSequenceDictionary().getSequence(1).getSequenceName();
}