@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(); }