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
private void init() throws IOException {
reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
dictionary = reference.getSequenceDictionary();
genomeLocParser = new GenomeLocParser(dictionary);
header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
header.setSequenceDictionary(dictionary);
header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
readGroup = new GATKSAMReadGroupRecord(header.getReadGroup("test"));
final List<GATKSAMRecord> reads = new ArrayList<>();
for (final String contig : contigs) {
for (int i = 1; i <= numReadsPerContig; i++) {
reads.add(buildSAMRecord("read" + contig + "_" + i, contig, i));
}
}
createBAM(reads);
}