@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);
}
public static GATKSAMRecord createRandomRead(int length, boolean allowNs) {
byte[] quals = ReadUtils.createRandomReadQuals(length);
byte[] bbases = ReadUtils.createRandomReadBases(length, allowNs);
return ArtificialSAMUtils.createArtificialRead(bbases, quals, bbases.length + "M");
}